HEADER LIGASE 14-AUG-08 3E5N TITLE CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM XANTHOMONAS TITLE 2 ORYZAE PV. ORYZAE KACC10331 COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANINE-D-ALANINE LIGASE A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE; SOURCE 3 ORGANISM_TAXID: 342109; SOURCE 4 STRAIN: MAFF 311018; SOURCE 5 GENE: XOO0324; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS BACTERIAL BLIGHT, D-ALANINE-D-ALANINE LIGASE, PIP (PLANT-INDUCIBLE KEYWDS 2 PROMOTER) BOX PEPTIDOGLYCAN BIOSYNTHESIS XANTHOMONAS ORYZAE PV. KEYWDS 3 ORYZAE, ATP-BINDING, CELL SHAPE, CELL WALL BIOGENESIS/DEGRADATION, KEYWDS 4 CYTOPLASM, LIGASE, MAGNESIUM, MANGANESE, METAL-BINDING, NUCLEOTIDE- KEYWDS 5 BINDING, PEPTIDOGLYCAN SYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR T.N.T.DOAN,J.K.KIM,H.S.KIM,Y.J.AHN,J.G.KIM,B.M.LEE,L.W.KANG REVDAT 3 01-NOV-23 3E5N 1 REMARK REVDAT 2 09-SEP-20 3E5N 1 TITLE JRNL SEQADV REVDAT 1 18-AUG-09 3E5N 0 JRNL AUTH T.N.T.DOAN,J.K.KIM,H.S.KIM,Y.J.AHN,J.G.KIM,B.M.LEE,L.W.KANG JRNL TITL CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM JRNL TITL 2 XANTHOMONAS ORYZAE PV. ORYZAE KACC10331 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 22572 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1217 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1623 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 83 REMARK 3 BIN FREE R VALUE : 0.2870 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2568 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.08000 REMARK 3 B22 (A**2) : -0.08000 REMARK 3 B33 (A**2) : 0.17000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.133 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.343 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2625 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3568 ; 2.002 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 341 ; 6.996 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;36.137 ;23.814 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 430 ;19.717 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;20.097 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 420 ; 0.176 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1992 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1223 ; 0.247 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1773 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 162 ; 0.193 ; 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): 59 ; 0.243 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.232 ; 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): 1748 ; 1.814 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2706 ; 2.686 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 974 ; 3.935 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 860 ; 5.682 ; 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): 2722 ; 2.834 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 142 ;10.371 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2582 ; 5.027 ; 3.000 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 : 1.20 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 3E5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048905. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : FLAT SI(111) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23816 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 2NMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15%(W/V) PEG4000, 0.1M TRIS, PH8.5, REMARK 280 0.2M MGCL2, 0.3M DIMETHYLETHYL-(3-SULFOPROPYL)-AMMONIUM, PH7.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 287K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 48.80050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.52150 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.52150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.20075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.52150 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.52150 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.40025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.52150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.52150 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.20075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.52150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.52150 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.40025 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 48.80050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.3 KCAL/MOL 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -48.80050 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 -18 REMARK 465 GLY A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLU A -7 REMARK 465 ASN A -6 REMARK 465 LEU A -5 REMARK 465 TYR A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 PRO A 92 REMARK 465 GLU A 93 REMARK 465 HIS A 250 REMARK 465 ASP A 251 REMARK 465 ALA A 252 REMARK 465 PHE A 253 REMARK 465 TYR A 254 REMARK 465 SER A 255 REMARK 465 TYR A 256 REMARK 465 ALA A 257 REMARK 465 THR A 258 REMARK 465 LYS A 259 REMARK 465 TYR A 260 REMARK 465 ILE A 261 REMARK 465 SER A 262 REMARK 465 GLU A 263 REMARK 465 HIS A 264 REMARK 465 GLY A 265 REMARK 465 ALA A 266 REMARK 465 ARG A 361 REMARK 465 SER A 362 REMARK 465 ALA A 363 REMARK 465 VAL A 364 REMARK 465 GLU A 365 REMARK 465 LEU A 366 REMARK 465 HIS A 367 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 O HOH A 398 O HOH A 439 2.12 REMARK 500 NE ARG A 25 O HOH A 425 2.17 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 ASP A 44 CB - CG - OD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 ARG A 146 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 ASP A 32 107.08 -55.39 REMARK 500 ASP A 44 164.33 -46.81 REMARK 500 SER A 56 43.52 -149.59 REMARK 500 GLN A 189 -160.29 75.13 REMARK 500 SER A 192 -78.16 79.58 REMARK 500 ASN A 236 -96.10 -100.31 REMARK 500 ASP A 308 -49.85 162.05 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 ASN A 188 GLN A 189 -146.28 REMARK 500 REMARK 500 REMARK: NULL DBREF 3E5N A 1 367 UNP Q2P8P8 Q2P8P8_XANOM 1 367 SEQADV 3E5N MET A -18 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N GLY A -17 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -16 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -15 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -14 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -13 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -12 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -11 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A -10 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N SER A -9 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N SER A -8 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N GLU A -7 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N ASN A -6 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N LEU A -5 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N TYR A -4 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N PHE A -3 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N GLN A -2 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N GLY A -1 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N HIS A 0 UNP Q2P8P8 EXPRESSION TAG SEQADV 3E5N VAL A 327 UNP Q2P8P8 MET 327 CONFLICT SEQRES 1 A 386 MET GLY HIS HIS HIS HIS HIS HIS HIS SER SER GLU ASN SEQRES 2 A 386 LEU TYR PHE GLN GLY HIS MET ARG LYS ILE ARG VAL GLY SEQRES 3 A 386 LEU ILE PHE GLY GLY LYS SER ALA GLU HIS GLU VAL SER SEQRES 4 A 386 LEU GLN SER ALA ARG ASN ILE LEU ASP ALA LEU ASP PRO SEQRES 5 A 386 GLN ARG PHE GLU PRO VAL LEU ILE GLY ILE ASP LYS GLN SEQRES 6 A 386 GLY GLN TRP HIS VAL ASN ASP PRO ASP SER PHE LEU LEU SEQRES 7 A 386 HIS ALA ASP ASP PRO ALA ARG ILE ALA LEU HIS ARG SER SEQRES 8 A 386 GLY ARG GLY VAL ALA LEU LEU PRO GLY ALA GLN GLN GLN SEQRES 9 A 386 GLN LEU ARG PRO ILE GLN PRO GLU GLN ALA LEU ALA GLN SEQRES 10 A 386 ILE ASP VAL VAL PHE PRO ILE VAL HIS GLY THR LEU GLY SEQRES 11 A 386 GLU ASP GLY SER LEU GLN GLY LEU LEU ARG MET ALA ASN SEQRES 12 A 386 LEU PRO PHE VAL GLY SER GLY VAL LEU GLY SER ALA VAL SEQRES 13 A 386 ALA MET ASP LYS ASP MET ALA LYS ARG VAL LEU ARG ASP SEQRES 14 A 386 ALA ARG LEU ALA VAL ALA PRO PHE VAL CYS PHE ASP ARG SEQRES 15 A 386 HIS THR ALA ALA HIS ALA ASP VAL ASP THR LEU ILE ALA SEQRES 16 A 386 GLN LEU GLY LEU PRO LEU PHE VAL LYS PRO ALA ASN GLN SEQRES 17 A 386 GLY SER SER VAL GLY VAL SER GLN VAL ARG THR ALA ASP SEQRES 18 A 386 ALA PHE ALA ALA ALA LEU ALA LEU ALA LEU ALA TYR ASP SEQRES 19 A 386 HIS LYS VAL LEU VAL GLU ALA ALA VAL ALA GLY ARG GLU SEQRES 20 A 386 ILE GLU CYS ALA VAL LEU GLY ASN ALA VAL PRO HIS ALA SEQRES 21 A 386 SER VAL CYS GLY GLU VAL VAL VAL HIS ASP ALA PHE TYR SEQRES 22 A 386 SER TYR ALA THR LYS TYR ILE SER GLU HIS GLY ALA GLU SEQRES 23 A 386 ILE VAL ILE PRO ALA ASP ILE ASP ALA GLN THR GLN GLN SEQRES 24 A 386 ARG ILE GLN GLN ILE ALA VAL GLN ALA TYR GLN ALA LEU SEQRES 25 A 386 GLY CYS ALA GLY MET ALA ARG VAL ASP VAL PHE LEU CYS SEQRES 26 A 386 ALA ASP GLY ARG ILE VAL ILE ASN GLU VAL ASN THR LEU SEQRES 27 A 386 PRO GLY PHE THR ARG ILE SER VAL TYR PRO LYS LEU TRP SEQRES 28 A 386 GLN ALA SER GLY LEU ASP TYR ARG GLY LEU ILE THR ARG SEQRES 29 A 386 LEU ILE GLU LEU ALA LEU GLU ARG HIS THR ASP ASP GLN SEQRES 30 A 386 LEU LEU ARG SER ALA VAL GLU LEU HIS FORMUL 2 HOH *142(H2 O) HELIX 1 1 GLU A 16 LEU A 31 1 16 HELIX 2 2 ASP A 53 SER A 56 5 4 HELIX 3 3 GLY A 108 ASP A 113 1 6 HELIX 4 4 GLY A 114 ALA A 123 1 10 HELIX 5 5 GLY A 131 ASP A 140 1 10 HELIX 6 6 ASP A 140 ALA A 151 1 12 HELIX 7 7 ARG A 163 ALA A 167 1 5 HELIX 8 8 ASP A 170 GLY A 179 1 10 HELIX 9 9 THR A 200 ASP A 202 5 3 HELIX 10 10 ALA A 203 LEU A 212 1 10 HELIX 11 11 ASP A 275 GLY A 294 1 20 HELIX 12 12 SER A 326 ALA A 334 1 9 HELIX 13 13 ASP A 338 LEU A 360 1 23 SHEET 1 A 4 TRP A 49 ASN A 52 0 SHEET 2 A 4 PHE A 36 ILE A 43 -1 N GLY A 42 O HIS A 50 SHEET 3 A 4 ILE A 4 GLY A 11 1 N PHE A 10 O ILE A 43 SHEET 4 A 4 VAL A 101 VAL A 106 1 O ILE A 105 N ILE A 9 SHEET 1 B 2 LEU A 58 LEU A 59 0 SHEET 2 B 2 ALA A 68 LEU A 69 -1 O ALA A 68 N LEU A 59 SHEET 1 C 2 VAL A 76 LEU A 78 0 SHEET 2 C 2 LEU A 87 PRO A 89 -1 O ARG A 88 N ALA A 77 SHEET 1 D 4 PHE A 158 ASP A 162 0 SHEET 2 D 4 LYS A 217 ALA A 222 -1 O VAL A 218 N PHE A 161 SHEET 3 D 4 LEU A 182 PRO A 186 -1 N LYS A 185 O LEU A 219 SHEET 4 D 4 SER A 196 VAL A 198 -1 O VAL A 198 N LEU A 182 SHEET 1 E 5 ILE A 268 VAL A 269 0 SHEET 2 E 5 HIS A 240 VAL A 247 -1 N GLU A 246 O VAL A 269 SHEET 3 E 5 ARG A 227 LEU A 234 -1 N LEU A 234 O HIS A 240 SHEET 4 E 5 MET A 298 LEU A 305 -1 O ALA A 299 N VAL A 233 SHEET 5 E 5 ILE A 311 ASN A 317 -1 O ASN A 317 N ARG A 300 CISPEP 1 LEU A 180 PRO A 181 0 6.97 CISPEP 2 ILE A 270 PRO A 271 0 -9.03 CISPEP 3 ALA A 307 ASP A 308 0 -7.22 CISPEP 4 ASP A 308 GLY A 309 0 -26.78 CRYST1 83.043 83.043 97.601 90.00 90.00 90.00 P 43 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 0.012042 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012042 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010246 0.00000