HEADER    HYDROLASE                               08-MAY-01   1ILW              
TITLE     CRYSTAL STRUCTURE OF PYRAZINAMIDASE/NICOTINAMIDASE OF PYROCOCCUS      
TITLE    2 HORIKOSHII                                                           
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 180 AA LONG HYPOTHETICAL PYRAZINAMIDASE/NICOTINAMIDASE;    
COMPND   3 CHAIN: A;                                                            
COMPND   4 EC: 3.5.1.19;                                                        
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII;                          
SOURCE   3 ORGANISM_TAXID: 53953;                                               
SOURCE   4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;                                 
SOURCE   5 EXPRESSION_SYSTEM_TAXID: 562;                                        
SOURCE   6 EXPRESSION_SYSTEM_STRAIN: B834(DE3)/SJS1244;                         
SOURCE   7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;                              
SOURCE   8 EXPRESSION_SYSTEM_PLASMID: PET21A                                    
KEYWDS    PYRAZINAMIDE, PYRAZINAMIDASE, NICOTINAMIDASE, TUBERCULOSIS,           
KEYWDS   2 HYDROLASE, CYSTEINE HYDROLASE, AMIDASE, STRUCTURAL GENOMICS, BSGC    
KEYWDS   3 STRUCTURE FUNDED BY NIH, PROTEIN STRUCTURE INITIATIVE, PSI, BERKELEY 
KEYWDS   4 STRUCTURAL GENOMICS CENTER                                           
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    X.DU,S.-H.KIM,BERKELEY STRUCTURAL GENOMICS CENTER (BSGC)              
REVDAT   6   03-APR-24 1ILW    1       REMARK                                   
REVDAT   5   07-FEB-24 1ILW    1       REMARK                                   
REVDAT   4   24-FEB-09 1ILW    1       VERSN                                    
REVDAT   3   25-JAN-05 1ILW    1       AUTHOR KEYWDS REMARK                     
REVDAT   2   24-AUG-04 1ILW    1       KEYWDS                                   
REVDAT   1   12-DEC-01 1ILW    0                                                
JRNL        AUTH   X.DU,W.WANG,R.KIM,H.YAKOTA,H.NGUYEN,S.-H.KIM                 
JRNL        TITL   CRYSTAL STRUCTURE AND MECHANISM OF CATALYSIS OF A            
JRNL        TITL 2 PYRAZINAMIDASE FROM PYROCOCCUS HORIKOSHII.                   
JRNL        REF    BIOCHEMISTRY                  V.  40 14166 2001              
JRNL        REFN                   ISSN 0006-2960                               
JRNL        PMID   11714269                                                     
JRNL        DOI    10.1021/BI0115479                                            
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.05 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : SHELXL-97                                            
REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 99.2                           
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
REMARK   3   FREE R VALUE TEST SET SELECTION   : NULL                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.189                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.181                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.257                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 9.800                  
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 954                    
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 9837                   
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL                   
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : NULL                   
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 1412                                          
REMARK   3   NUCLEIC ACID ATOMS : 0                                             
REMARK   3   HETEROGEN ATOMS    : 0                                             
REMARK   3   SOLVENT ATOMS      : 88                                            
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL                    
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL                    
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL                    
REMARK   3   NUMBER OF RESTRAINTS                     : NULL                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : NULL                    
REMARK   3   ANGLE DISTANCES                      (A) : NULL                    
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL                    
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL                    
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL                    
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL                    
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL                    
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL                    
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL                    
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL                    
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: NULL                                                  
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH $ HUBER                        
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1ILW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-01.                  
REMARK 100 THE DEPOSITION ID IS D_1000013396.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 01-MAR-00                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 4.6                                
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : SSRL                               
REMARK 200  BEAMLINE                       : BL7-1                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.08                               
REMARK 200  MONOCHROMATOR                  : GRAPHITE                           
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : MARRESEARCH                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 9862                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.050                              
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     (%) : 99.2                               
REMARK 200  DATA REDUNDANCY                : 4.246                              
REMARK 200  R MERGE                    (I) : 0.02900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 42.5000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.11                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 88.0                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 3.10                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.11800                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 17.40                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: SOLVE                                                 
REMARK 200 STARTING MODEL: A STRUCTURE OF THE SAME PROTEIN OBTAINED ON MAD      
REMARK 200  DATA                                                                
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 36.46                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 22.5% PEG3350, 250 MM AMMONIUM           
REMARK 280  ACETATE, 100 MM SODIUM ACETATE, PH 4.6. SEEDING., VAPOR             
REMARK 280  DIFFUSION, HANGING DROP, TEMPERATURE 298K                           
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1                         
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,Y+1/2,-Z                                             
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       21.70900            
REMARK 290   SMTRY3   2  0.000000  0.000000 -1.000000        0.00000            
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 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     MET A     1                                                      
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
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   RES CSSEQI ATM2   DEVIATION                     
REMARK 500    PHE A 180   C     PHE A 180   O       0.219                       
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    ALA A 102      101.60   -166.06                                   
REMARK 500    TYR A 132      -96.73   -117.62                                   
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: BSGCAIR30510   RELATED DB: TARGETDB                      
DBREF  1ILW A    1   180  UNP    O58727   O58727_PYRHO     1    180             
SEQRES   1 A  180  MET PRO GLU GLU ALA LEU ILE VAL VAL ASP MET GLN ARG          
SEQRES   2 A  180  ASP PHE MET PRO GLY GLY ALA LEU PRO VAL PRO GLU GLY          
SEQRES   3 A  180  ASP LYS ILE ILE PRO LYS VAL ASN GLU TYR ILE ARG LYS          
SEQRES   4 A  180  PHE LYS GLU LYS GLY ALA LEU ILE VAL ALA THR ARG ASP          
SEQRES   5 A  180  TRP HIS PRO GLU ASN HIS ILE SER PHE ARG GLU ARG GLY          
SEQRES   6 A  180  GLY PRO TRP PRO ARG HIS CYS VAL GLN ASN THR PRO GLY          
SEQRES   7 A  180  ALA GLU PHE VAL VAL ASP LEU PRO GLU ASP ALA VAL ILE          
SEQRES   8 A  180  ILE SER LYS ALA THR GLU PRO ASP LYS GLU ALA TYR SER          
SEQRES   9 A  180  GLY PHE GLU GLY THR ASP LEU ALA LYS ILE LEU ARG GLY          
SEQRES  10 A  180  ASN GLY VAL LYS ARG VAL TYR ILE CYS GLY VAL ALA THR          
SEQRES  11 A  180  GLU TYR CYS VAL ARG ALA THR ALA LEU ASP ALA LEU LYS          
SEQRES  12 A  180  HIS GLY PHE GLU VAL TYR LEU LEU ARG ASP ALA VAL LYS          
SEQRES  13 A  180  GLY ILE LYS PRO GLU ASP GLU GLU ARG ALA LEU GLU GLU          
SEQRES  14 A  180  MET LYS SER ARG GLY ILE LYS ILE VAL GLN PHE                  
FORMUL   2  HOH   *88(H2 O)                                                     
HELIX    1   1 ARG A   13  MET A   16  5                                   4    
HELIX    2   2 GLU A   25  LYS A   28  5                                   4    
HELIX    3   3 ILE A   29  LYS A   43  1                                  15    
HELIX    4   4 ARG A   62  GLY A   65  5                                   4    
HELIX    5   5 THR A   76  GLU A   80  5                                   5    
HELIX    6   6 ASP A  110  ASN A  118  1                                   9    
HELIX    7   7 TYR A  132  HIS A  144  1                                  13    
HELIX    8   8 LYS A  159  GLY A  174  1                                  16    
SHEET    1   A 6 VAL A  90  LYS A  94  0                                        
SHEET    2   A 6 LEU A  46  ASP A  52  1  O  ILE A  47   N  VAL A  90           
SHEET    3   A 6 GLU A   4  VAL A   9  1  O  GLU A   4   N  LEU A  46           
SHEET    4   A 6 ARG A 122  VAL A 128  1  O  ARG A 122   N  ALA A   5           
SHEET    5   A 6 GLU A 147  LYS A 156  1  O  GLU A 147   N  VAL A 123           
SHEET    6   A 6 LYS A 176  VAL A 178  1  O  LYS A 176   N  LEU A 150           
CISPEP   1 VAL A  128    ALA A  129          0       -14.28                     
CRYST1   32.977   43.418   55.781  90.00 101.22  90.00 P 1 21 1      2          
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      0.030324  0.000000  0.006014        0.00000                         
SCALE2      0.000000  0.023032  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.018276        0.00000