HEADER    LIGASE                                  24-FEB-09   3GDE              
TITLE     THE CLOSED CONFORMATION OF ATP-DEPENDENT DNA LIGASE FROM ARCHAEOGLOBUS
TITLE    2 FULGIDUS                                                             
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: DNA LIGASE;                                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: ATP-DEPENDENT DNA LIGASE, POLYDEOXYRIBONUCLEOTIDE SYNTHASE  
COMPND   5 [ATP];                                                               
COMPND   6 EC: 6.5.1.1;                                                         
COMPND   7 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: ARCHAEOGLOBUS FULGIDUS;                         
SOURCE   3 ORGANISM_TAXID: 2234;                                                
SOURCE   4 GENE: AF0623;                                                        
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3) PLYSS;                       
SOURCE   8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   9 EXPRESSION_SYSTEM_PLASMID: PET28B                                    
KEYWDS    ATP-DEPENDENT DNA LIGASE, DNA-BINDING DOMAIN, ADENYLATION DOMAIN, OB- 
KEYWDS   2 FOLD DOMAIN, ATP-BINDING, CELL CYCLE, CELL DIVISION, DNA DAMAGE, DNA 
KEYWDS   3 RECOMBINATION, DNA REPAIR, DNA REPLICATION, LIGASE, NUCLEOTIDE-      
KEYWDS   4 BINDING                                                              
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    D.J.KIM,H.-W.KIM,O.KIM,H.S.KIM,S.J.LEE,S.W.SUH                        
REVDAT   3   01-NOV-23 3GDE    1       REMARK SEQADV                            
REVDAT   2   01-NOV-17 3GDE    1       REMARK                                   
REVDAT   1   15-DEC-09 3GDE    0                                                
JRNL        AUTH   D.J.KIM,O.KIM,H.-W.KIM,H.S.KIM,S.J.LEE,S.W.SUH               
JRNL        TITL   ATP-DEPENDENT DNA LIGASE FROM ARCHAEOGLOBUS FULGIDUS         
JRNL        TITL 2 DISPLAYS A TIGHTLY CLOSED CONFORMATION                       
JRNL        REF    ACTA CRYSTALLOGR.,SECT.F      V.  65   544 2009              
JRNL        REFN                   ESSN 1744-3091                               
JRNL        PMID   19478428                                                     
JRNL        DOI    10.1107/S1744309109017485                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.30 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : REFMAC 5.2.0019                                      
REMARK   3   AUTHORS     : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,              
REMARK   3               : NICHOLLS,WINN,LONG,VAGIN                             
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : MAXIMUM LIKELIHOOD                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.8                           
REMARK   3   NUMBER OF REFLECTIONS             : 36294                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.221                           
REMARK   3   R VALUE            (WORKING SET) : 0.215                           
REMARK   3   FREE R VALUE                     : 0.277                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 9.900                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 4007                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 20                           
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 2.30                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 2.36                         
REMARK   3   REFLECTION IN BIN     (WORKING SET) : 2625                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 99.79                        
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2500                       
REMARK   3   BIN FREE R VALUE SET COUNT          : 255                          
REMARK   3   BIN FREE R VALUE                    : 0.3510                       
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 4423                                    
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 20                                      
REMARK   3   SOLVENT ATOMS            : 458                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 37.04                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : 1.62000                                              
REMARK   3    B22 (A**2) : 1.62000                                              
REMARK   3    B33 (A**2) : -3.25000                                             
REMARK   3    B12 (A**2) : 0.00000                                              
REMARK   3    B13 (A**2) : 0.00000                                              
REMARK   3    B23 (A**2) : 0.00000                                              
REMARK   3                                                                      
REMARK   3  ESTIMATED OVERALL COORDINATE ERROR.                                 
REMARK   3   ESU BASED ON R VALUE                            (A): 0.278         
REMARK   3   ESU BASED ON FREE R VALUE                       (A): 0.243         
REMARK   3   ESU BASED ON MAXIMUM LIKELIHOOD                 (A): 0.169         
REMARK   3   ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.916         
REMARK   3                                                                      
REMARK   3 CORRELATION COEFFICIENTS.                                            
REMARK   3   CORRELATION COEFFICIENT FO-FC      : 0.939                         
REMARK   3   CORRELATION COEFFICIENT FO-FC FREE : 0.900                         
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT      
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):  4513 ; 0.010 ; 0.022       
REMARK   3   BOND LENGTHS OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):  6073 ; 1.314 ; 1.988       
REMARK   3   BOND ANGLES OTHERS          (DEGREES):  NULL ;  NULL ;  NULL       
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):   549 ; 7.246 ; 5.000       
REMARK   3   TORSION ANGLES, PERIOD 2    (DEGREES):   204 ;36.166 ;23.382       
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   874 ;18.920 ;15.000       
REMARK   3   TORSION ANGLES, PERIOD 4    (DEGREES):    42 ;19.356 ;15.000       
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   678 ; 0.098 ; 0.200       
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):  3309 ; 0.004 ; 0.020       
REMARK   3   GENERAL PLANES OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):  2322 ; 0.198 ; 0.200       
REMARK   3   NON-BONDED CONTACTS OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   NON-BONDED TORSION REFINED ATOMS  (A):  3087 ; 0.299 ; 0.200       
REMARK   3   NON-BONDED TORSION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):   420 ; 0.153 ; 0.200       
REMARK   3   H-BOND (X...Y) OTHERS             (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION REFINED ATOMS (A):  NULL ;  NULL ;  NULL       
REMARK   3   POTENTIAL METAL-ION OTHERS        (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    57 ; 0.235 ; 0.200       
REMARK   3   SYMMETRY VDW OTHERS               (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    28 ; 0.187 ; 0.200       
REMARK   3   SYMMETRY H-BOND OTHERS            (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION REFINED ATOMS  (A):  NULL ;  NULL ;  NULL       
REMARK   3   SYMMETRY METAL-ION OTHERS         (A):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.     COUNT   RMS    WEIGHT      
REMARK   3   MAIN-CHAIN BOND REFINED ATOMS  (A**2):  2823 ; 0.683 ; 1.500       
REMARK   3   MAIN-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   MAIN-CHAIN ANGLE REFINED ATOMS (A**2):  4418 ; 1.189 ; 2.000       
REMARK   3   MAIN-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN BOND REFINED ATOMS  (A**2):  1896 ; 1.622 ; 3.000       
REMARK   3   SIDE-CHAIN BOND OTHER ATOMS    (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SIDE-CHAIN ANGLE REFINED ATOMS (A**2):  1655 ; 2.765 ; 4.500       
REMARK   3   SIDE-CHAIN ANGLE OTHER ATOMS   (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B REFINED ATOMS     (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   LONG RANGE B OTHER ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3 ANISOTROPIC THERMAL FACTOR RESTRAINTS.    COUNT   RMS   WEIGHT       
REMARK   3   RIGID-BOND RESTRAINTS          (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; FREE ATOMS         (A**2):  NULL ;  NULL ;  NULL       
REMARK   3   SPHERICITY; BONDED ATOMS       (A**2):  NULL ;  NULL ;  NULL       
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS STATISTICS                                           
REMARK   3   NUMBER OF DIFFERENT NCS GROUPS : NULL                              
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : NULL                                       
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED : MASK                                                 
REMARK   3   PARAMETERS FOR MASK CALCULATION                                    
REMARK   3   VDW PROBE RADIUS   : 1.40                                          
REMARK   3   ION PROBE RADIUS   : 0.80                                          
REMARK   3   SHRINKAGE RADIUS   : 0.80                                          
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING   
REMARK   3  POSITIONS                                                           
REMARK   4                                                                      
REMARK   4 3GDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-09.                  
REMARK 100 THE DEPOSITION ID IS D_1000051720.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 01-JAN-06                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 9.0                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : PAL/PLS                            
REMARK 200  BEAMLINE                       : 4A                                 
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.0000                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : ADSC QUANTUM 210                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000                    
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 40500                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.300                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : 0.08900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 36.0000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.38                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 100.0                              
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.44000                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 5.100                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: PHASER                                                
REMARK 200 STARTING MODEL: PDB ENTRY 2CFM                                       
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 64.21                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.44                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, PH9.0, 0.4M SODIUM       
REMARK 280  DIHYDROGEN PHOSPHATE, 1.2M DIPOTASSIUM HYDROGEN PHOSPHATE, 10MM     
REMARK 280  MAGNESIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE      
REMARK 280  294K                                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y+1/2,X+1/2,Z+1/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+3/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+1/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+3/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290   SMTRY1   2 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       98.70800            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       47.17750            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       47.17750            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       49.35400            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       47.17750            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       47.17750            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000      148.06200            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       47.17750            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       47.17750            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       49.35400            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       47.17750            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       47.17750            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000      148.06200            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       98.70800            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC                  
REMARK 350 SOFTWARE USED: PISA                                                  
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 465                                                                      
REMARK 465 MISSING RESIDUES                                                     
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE                       
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)                
REMARK 465                                                                      
REMARK 465   M RES C SSSEQI                                                     
REMARK 465     LYS A   320                                                      
REMARK 465     HIS A   321                                                      
REMARK 465     GLU A   551                                                      
REMARK 465     VAL A   552                                                      
REMARK 465     LYS A   553                                                      
REMARK 465     ARG A   554                                                      
REMARK 465     GLN A   555                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT                     
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500   OE2  GLU A   110     O    HOH A   974              2.05            
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500    ARG A 411   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.3 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: TORSION ANGLES                                             
REMARK 500                                                                      
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:            
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                             
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)                    
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-           
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400            
REMARK 500                                                                      
REMARK 500  M RES CSSEQI        PSI       PHI                                   
REMARK 500    GLU A 111      134.95    112.63                                   
REMARK 500    HIS A 220       -3.14     84.37                                   
REMARK 500    TRP A 259      129.83   -179.42                                   
REMARK 500    ASP A 260      -79.44    179.59                                   
REMARK 500    ASP A 343       62.80     38.51                                   
REMARK 500    CYS A 346       14.60   -144.89                                   
REMARK 500    PRO A 350       95.80     32.11                                   
REMARK 500    SER A 365     -169.10   -128.73                                   
REMARK 500    HIS A 394     -168.67   -105.44                                   
REMARK 500    ARG A 411       75.99   -117.11                                   
REMARK 500    ARG A 439        5.93    -66.06                                   
REMARK 500    LYS A 497      -55.60   -158.45                                   
REMARK 500    VAL A 525      -61.55    -98.06                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS                                         
REMARK 500                                                                      
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH          
REMARK 500 CIS AND TRANS CONFORMATION.  CIS BONDS, IF ANY, ARE LISTED           
REMARK 500 ON CISPEP RECORDS.  TRANS IS DEFINED AS 180 +/- 30 AND               
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.                                  
REMARK 500                                 MODEL     OMEGA                      
REMARK 500 LEU A  349     PRO A  350                   81.10                    
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 556                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 557                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC3                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 558                 
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC4                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 559                 
DBREF  3GDE A    1   555  UNP    O29632   DNLI_ARCFU       1    555             
SEQADV 3GDE GLY A   -2  UNP  O29632              EXPRESSION TAG                 
SEQADV 3GDE SER A   -1  UNP  O29632              EXPRESSION TAG                 
SEQADV 3GDE HIS A    0  UNP  O29632              EXPRESSION TAG                 
SEQRES   1 A  558  GLY SER HIS MET LEU PHE ALA GLU PHE ALA GLU PHE CYS          
SEQRES   2 A  558  GLU ARG LEU GLU LYS ILE SER SER THR LEU GLU LEU THR          
SEQRES   3 A  558  ALA ARG ILE ALA ALA PHE LEU GLN LYS ILE GLU ASP GLU          
SEQRES   4 A  558  ARG ASP LEU TYR ASP VAL VAL LEU PHE ILE THR GLY LYS          
SEQRES   5 A  558  VAL TYR PRO PRO TRP ASP GLU ARG GLU LEU GLY VAL GLY          
SEQRES   6 A  558  ILE GLY LEU LEU TYR GLU ALA LEU GLU ASN VAL SER GLY          
SEQRES   7 A  558  VAL LYS ARG SER GLU ILE GLU SER MET ILE ARG GLU TYR          
SEQRES   8 A  558  GLY ASP LEU GLY LEU VAL ALA GLU GLN LEU ILE LYS LYS          
SEQRES   9 A  558  LYS LYS MET THR THR LEU ALA PHE GLU GLU LEU THR VAL          
SEQRES  10 A  558  ARG LYS VAL ARG GLU THR PHE ASP GLU ILE ALA SER LEU          
SEQRES  11 A  558  THR GLY GLU GLY SER MET LYS ARG LYS ILE MET LEU LEU          
SEQRES  12 A  558  THR GLY LEU TYR GLY LEU ALA THR PRO LEU GLU ALA ARG          
SEQRES  13 A  558  TYR LEU THR ARG LEU ILE LEU ASN GLU MET ARG LEU GLY          
SEQRES  14 A  558  VAL GLY GLU GLY ILE MET ARG ASP ALA ILE ALA ARG ALA          
SEQRES  15 A  558  PHE ARG ALA ASP PRO GLU THR VAL GLU ARG ALA TYR MET          
SEQRES  16 A  558  ILE THR ASN ASP LEU GLY ARG VAL ALA VAL VAL ALA LYS          
SEQRES  17 A  558  LYS GLU GLY GLU GLU GLY LEU ARG LYS MET LYS ILE GLU          
SEQRES  18 A  558  ILE HIS ILE PRO VAL ARG MET MET LEU ALA GLN VAL ALA          
SEQRES  19 A  558  GLU SER LEU GLU SER ALA VAL ARG GLU MET ARG THR ALA          
SEQRES  20 A  558  ALA VAL GLU TRP LYS PHE ASP GLY SER ARG VAL GLN VAL          
SEQRES  21 A  558  HIS TRP ASP GLY SER ARG VAL THR ILE TYR SER ARG ARG          
SEQRES  22 A  558  LEU GLU ASN VAL THR ASN ALA LEU PRO ASP ILE VAL GLU          
SEQRES  23 A  558  GLU ILE LYS LYS SER VAL LYS PRO GLY VAL ILE LEU ASP          
SEQRES  24 A  558  GLY GLU VAL ILE ALA VAL LYS GLU GLY LYS PRO MET PRO          
SEQRES  25 A  558  PHE GLN HIS VAL LEU ARG ARG PHE ARG ARG LYS HIS ASP          
SEQRES  26 A  558  VAL ALA LYS MET VAL GLU LYS ILE PRO LEU GLU ALA HIS          
SEQRES  27 A  558  PHE PHE ASP ILE LEU TYR HIS ASP GLY GLU CYS ILE ASP          
SEQRES  28 A  558  LEU PRO LEU ARG GLU ARG ARG LYS LEU LEU GLU SER ALA          
SEQRES  29 A  558  VAL ASN GLU SER GLU LYS ILE LYS LEU ALA LYS GLN ILE          
SEQRES  30 A  558  VAL THR ASP SER VAL ASP GLU VAL ARG LYS MET TYR ASP          
SEQRES  31 A  558  GLU ALA ILE SER ALA GLY HIS GLU GLY VAL MET ILE LYS          
SEQRES  32 A  558  LEU PRO SER SER PRO TYR ILE PRO GLY LYS ARG GLY LYS          
SEQRES  33 A  558  ASN TRP LEU LYS VAL LYS ALA ILE MET GLU THR LEU ASP          
SEQRES  34 A  558  LEU VAL VAL VAL GLY GLY GLU TRP GLY GLU GLY LYS ARG          
SEQRES  35 A  558  SER HIS TRP LEU SER SER PHE GLU LEU ALA CYS LEU ASP          
SEQRES  36 A  558  PRO VAL THR GLY LYS LEU LEU LYS VAL GLY ARG VAL ALA          
SEQRES  37 A  558  THR GLY PHE THR GLU GLU ASP LEU GLU GLU LEU THR GLU          
SEQRES  38 A  558  MET PHE ARG PRO LEU ILE VAL SER GLN GLN GLY LYS LYS          
SEQRES  39 A  558  VAL GLU PHE ILE PRO LYS TYR VAL PHE GLU VAL ALA TYR          
SEQRES  40 A  558  GLN GLU ILE GLN LYS SER PRO LYS TYR GLU SER GLY TYR          
SEQRES  41 A  558  ALA LEU ARG PHE PRO ARG PHE VAL ARG LEU ARG ASP ASP          
SEQRES  42 A  558  LYS ASP VAL ASP GLU ALA ASP THR ILE GLU ARG VAL GLU          
SEQRES  43 A  558  ASN LEU TYR LYS LEU GLN PHE GLU VAL LYS ARG GLN              
HET    PO4  A 556       5                                                       
HET    PO4  A 557       5                                                       
HET    PO4  A 558       5                                                       
HET    PO4  A 559       5                                                       
HETNAM     PO4 PHOSPHATE ION                                                    
FORMUL   2  PO4    4(O4 P 3-)                                                   
FORMUL   6  HOH   *458(H2 O)                                                    
HELIX    1   1 LEU A    2  GLU A   14  1                                  13    
HELIX    2   2 SER A   18  LYS A   32  1                                  15    
HELIX    3   3 ASP A   35  THR A   47  1                                  13    
HELIX    4   4 GLY A   62  GLY A   75  1                                  14    
HELIX    5   5 LYS A   77  GLY A   89  1                                  13    
HELIX    6   6 ASP A   90  THR A  106  1                                  17    
HELIX    7   7 THR A  113  LEU A  127  1                                  15    
HELIX    8   8 GLY A  131  ALA A  147  1                                  17    
HELIX    9   9 THR A  148  LEU A  160  1                                  13    
HELIX   10  10 GLY A  168  PHE A  180  1                                  13    
HELIX   11  11 ASP A  183  ASN A  195  1                                  13    
HELIX   12  12 ASP A  196  LYS A  214  1                                  19    
HELIX   13  13 SER A  233  MET A  241  1                                   9    
HELIX   14  14 VAL A  274  ALA A  277  5                                   4    
HELIX   15  15 LEU A  278  VAL A  289  1                                  12    
HELIX   16  16 PRO A  309  ARG A  319  1                                  11    
HELIX   17  17 VAL A  323  ILE A  330  1                                   8    
HELIX   18  18 PRO A  350  VAL A  362  1                                  13    
HELIX   19  19 SER A  378  ALA A  392  1                                  15    
HELIX   20  20 LYS A  438  HIS A  441  5                                   4    
HELIX   21  21 THR A  469  ARG A  481  1                                  13    
HELIX   22  22 ASP A  532  ALA A  536  5                                   5    
HELIX   23  23 THR A  538  LEU A  548  1                                  11    
SHEET    1   A 5 LEU A 227  VAL A 230  0                                        
SHEET    2   A 5 ARG A 411  LYS A 419  1  O  LYS A 417   N  GLN A 229           
SHEET    3   A 5 GLY A 396  LYS A 400 -1  N  ILE A 399   O  LEU A 416           
SHEET    4   A 5 ALA A 244  LYS A 249 -1  N  ALA A 245   O  LYS A 400           
SHEET    5   A 5 GLN A 373  THR A 376 -1  O  ILE A 374   N  VAL A 246           
SHEET    1   B 4 THR A 265  SER A 268  0                                        
SHEET    2   B 4 SER A 253  TRP A 259 -1  N  HIS A 258   O  THR A 265           
SHEET    3   B 4 VAL A 293  LYS A 303 -1  O  VAL A 293   N  TRP A 259           
SHEET    4   B 4 LYS A 306  MET A 308 -1  O  MET A 308   N  ALA A 301           
SHEET    1   C 5 THR A 265  SER A 268  0                                        
SHEET    2   C 5 SER A 253  TRP A 259 -1  N  HIS A 258   O  THR A 265           
SHEET    3   C 5 VAL A 293  LYS A 303 -1  O  VAL A 293   N  TRP A 259           
SHEET    4   C 5 LEU A 332  HIS A 342 -1  O  LEU A 340   N  ILE A 294           
SHEET    5   C 5 ILE A 368  LEU A 370  1  O  LYS A 369   N  ALA A 334           
SHEET    1   D 5 LEU A 458  VAL A 464  0                                        
SHEET    2   D 5 LEU A 443  LEU A 451 -1  N  LEU A 448   O  VAL A 461           
SHEET    3   D 5 LEU A 425  TRP A 434 -1  N  GLU A 433   O  SER A 444           
SHEET    4   D 5 LYS A 491  PHE A 494 -1  O  PHE A 494   N  VAL A 430           
SHEET    5   D 5 ILE A 484  GLN A 488 -1  N  GLN A 488   O  LYS A 491           
SHEET    1   E 5 LEU A 458  VAL A 464  0                                        
SHEET    2   E 5 LEU A 443  LEU A 451 -1  N  LEU A 448   O  VAL A 461           
SHEET    3   E 5 LEU A 425  TRP A 434 -1  N  GLU A 433   O  SER A 444           
SHEET    4   E 5 VAL A 499  ALA A 503 -1  O  VAL A 502   N  LEU A 425           
SHEET    5   E 5 ARG A 523  LEU A 527 -1  O  ARG A 526   N  GLU A 501           
SHEET    1   F 2 GLU A 506  LYS A 509  0                                        
SHEET    2   F 2 TYR A 517  ARG A 520 -1  O  ARG A 520   N  GLU A 506           
CISPEP   1 TRP A  259    ASP A  260          0       -29.94                     
CISPEP   2 ASP A  260    GLY A  261          0         4.69                     
SITE     1 AC1  9 ARG A 269  ARG A 411  LYS A 417  PO4 A 557                    
SITE     2 AC1  9 HOH A 586  HOH A 587  HOH A 692  HOH A 890                    
SITE     3 AC1  9 HOH A 893                                                     
SITE     1 AC2 10 LYS A 249  GLU A 395  LYS A 417  LYS A 419                    
SITE     2 AC2 10 GLU A 423  PO4 A 556  PO4 A 558  HOH A 870                    
SITE     3 AC2 10 HOH A 971  HOH A1012                                          
SITE     1 AC3  8 ARG A 528  LYS A 531  PO4 A 557  HOH A 730                    
SITE     2 AC3  8 HOH A 890  HOH A 904  HOH A 990  HOH A1012                    
SITE     1 AC4  4 GLN A 311  ARG A 526  HOH A 748  HOH A 866                    
CRYST1   94.355   94.355  197.416  90.00  90.00  90.00 P 41 21 2     8          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.010598  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.010598  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.005065        0.00000