HEADER TRANSFERASE 11-SEP-12 4BA5 TITLE CRYSTAL STRUCTURE OF OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.6.1.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHROMOBACTERIUM VIOLACEUM; SOURCE 3 ORGANISM_TAXID: 536; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.SAYER,M.N.ISUPOV,J.A.LITTLECHILD REVDAT 3 20-DEC-23 4BA5 1 REMARK REVDAT 2 03-APR-13 4BA5 1 JRNL REVDAT 1 27-MAR-13 4BA5 0 JRNL AUTH C.SAYER,M.N.ISUPOV,A.WESTLAKE,J.A.LITTLECHILD JRNL TITL STRUCTURAL STUDIES WITH PSEUDOMONAS AND CHROMOBACTERIUM JRNL TITL 2 [OMEGA]-AMINOTRANSFERASES PROVIDE INSIGHTS INTO THEIR JRNL TITL 3 DIFFERING SUBSTRATE SPECIFICITY. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 69 564 2013 JRNL REFN ISSN 0907-4449 JRNL PMID 23519665 JRNL DOI 10.1107/S0907444912051670 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 65355 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 135 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2910 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 53.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3760 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6702 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 582 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.52000 REMARK 3 B12 (A**2) : -0.51000 REMARK 3 B13 (A**2) : 1.27000 REMARK 3 B23 (A**2) : -0.47000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.170 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4BA5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1290054044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.49 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65355 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 41.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.6 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 52.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4AH3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 7730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 GLN A 2 REMARK 465 LYS A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 THR A 6 REMARK 465 THR A 7 REMARK 465 SER A 8 REMARK 465 GLN A 9 REMARK 465 TRP A 10 REMARK 465 ARG A 11 REMARK 465 GLU A 12 REMARK 465 LEU A 13 REMARK 465 ASP A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 LEU A 19 REMARK 465 HIS A 20 REMARK 465 PRO A 21 REMARK 465 PHE A 22 REMARK 465 THR A 23 REMARK 465 ASP A 24 REMARK 465 THR A 25 REMARK 465 ALA A 26 REMARK 465 SER A 27 REMARK 465 LEU A 28 REMARK 465 ASN A 29 REMARK 465 GLN A 30 REMARK 465 ALA A 31 REMARK 465 GLY A 32 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 LYS B 3 REMARK 465 GLN B 4 REMARK 465 ARG B 5 REMARK 465 THR B 6 REMARK 465 THR B 7 REMARK 465 SER B 8 REMARK 465 GLN B 9 REMARK 465 TRP B 10 REMARK 465 ARG B 11 REMARK 465 GLU B 12 REMARK 465 LEU B 13 REMARK 465 ASP B 14 REMARK 465 ALA B 15 REMARK 465 ALA B 16 REMARK 465 HIS B 17 REMARK 465 HIS B 18 REMARK 465 LEU B 19 REMARK 465 HIS B 20 REMARK 465 PRO B 21 REMARK 465 PHE B 22 REMARK 465 THR B 23 REMARK 465 ASP B 24 REMARK 465 THR B 25 REMARK 465 ALA B 26 REMARK 465 SER B 27 REMARK 465 LEU B 28 REMARK 465 ASN B 29 REMARK 465 GLN B 30 REMARK 465 ALA B 31 REMARK 465 GLY B 32 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 CA LYS B 386 O HOH B 2246 0.62 REMARK 500 C LYS B 386 O HOH B 2246 1.04 REMARK 500 N LYS B 386 O HOH B 2246 1.57 REMARK 500 OD1 ASP B 406 O HOH B 2252 1.66 REMARK 500 NH2 ARG B 405 O HOH B 2252 1.85 REMARK 500 O LYS B 386 O HOH B 2246 1.96 REMARK 500 N ASN B 387 O HOH B 2246 2.01 REMARK 500 CB LYS B 386 O HOH B 2246 2.04 REMARK 500 O HOH B 2170 O HOH B 2171 2.08 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 421 CG HIS A 421 CD2 0.055 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 LEU B 283 CA - CB - CG ANGL. DEV. = 13.9 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 ALA A 57 82.33 41.09 REMARK 500 TRP A 60 -7.03 67.35 REMARK 500 TYR A 85 -61.62 164.26 REMARK 500 ASN A 86 -167.86 50.85 REMARK 500 THR A 87 -138.72 -144.06 REMARK 500 PHE A 88 122.33 -20.19 REMARK 500 ASP A 174 64.92 37.48 REMARK 500 ASP A 174 68.29 33.30 REMARK 500 LYS A 193 -125.21 48.08 REMARK 500 ALA A 287 -118.38 -137.55 REMARK 500 ASP A 351 -76.88 -124.40 REMARK 500 ASP A 351 -75.99 -124.94 REMARK 500 PHE A 397 119.62 -37.42 REMARK 500 LEU B 59 69.62 -119.23 REMARK 500 TRP B 60 28.12 46.46 REMARK 500 PHE B 89 -110.23 56.22 REMARK 500 GLU B 171 45.30 165.59 REMARK 500 GLU B 171 -98.43 55.98 REMARK 500 GLN B 172 42.65 30.02 REMARK 500 ASP B 174 95.00 69.94 REMARK 500 LYS B 193 -122.93 45.46 REMARK 500 ALA B 287 -142.74 -125.96 REMARK 500 ALA B 312 -7.39 -59.41 REMARK 500 ASP B 315 -84.64 -123.30 REMARK 500 ASN B 317 -91.66 -121.97 REMARK 500 HIS B 318 85.88 -55.12 REMARK 500 PHE B 320 -71.37 -86.83 REMARK 500 SER B 323 -30.46 -147.34 REMARK 500 SER B 323 -31.85 -146.74 REMARK 500 ASP B 351 -72.21 -134.77 REMARK 500 ALA B 425 83.50 -151.50 REMARK 500 ALA B 455 12.99 -66.68 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 THR A 87 PHE A 88 -101.44 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 PXG A 470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXG B 470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1460 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4A6R RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM REMARK 900 VIOLACEUM IN THE APO FORM, CRYSTALLISED FROM POLYACRYLIC ACID REMARK 900 RELATED ID: 4A6T RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM REMARK 900 VIOLACEUM IN COMPLEX WITH PLP REMARK 900 RELATED ID: 4A6U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM REMARK 900 VIOLACEUM IN THE APO FORM, CRYSTALLISED FROM PEG 3350 REMARK 900 RELATED ID: 4A72 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM REMARK 900 VIOLACEUM IN A MIXTURE OF APO AND PLP -BOUND STATES REMARK 900 RELATED ID: 4AH3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HOLO OMEGA-TRANSAMINASE FROM REMARK 900 CHROMOBACTERIUM VIOLACEUM REMARK 900 RELATED ID: 4BA4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APO OMEGA-TRANSAMINASE FROM REMARK 900 CHROMOBACTERIUM VIOLACEUM DBREF 4BA5 A 1 459 UNP Q7NWG4 Q7NWG4_CHRVO 1 459 DBREF 4BA5 B 1 459 UNP Q7NWG4 Q7NWG4_CHRVO 1 459 SEQRES 1 A 459 MET GLN LYS GLN ARG THR THR SER GLN TRP ARG GLU LEU SEQRES 2 A 459 ASP ALA ALA HIS HIS LEU HIS PRO PHE THR ASP THR ALA SEQRES 3 A 459 SER LEU ASN GLN ALA GLY ALA ARG VAL MET THR ARG GLY SEQRES 4 A 459 GLU GLY VAL TYR LEU TRP ASP SER GLU GLY ASN LYS ILE SEQRES 5 A 459 ILE ASP GLY MET ALA GLY LEU TRP CYS VAL ASN VAL GLY SEQRES 6 A 459 TYR GLY ARG LYS ASP PHE ALA GLU ALA ALA ARG ARG GLN SEQRES 7 A 459 MET GLU GLU LEU PRO PHE TYR ASN THR PHE PHE LYS THR SEQRES 8 A 459 THR HIS PRO ALA VAL VAL GLU LEU SER SER LEU LEU ALA SEQRES 9 A 459 GLU VAL THR PRO ALA GLY PHE ASP ARG VAL PHE TYR THR SEQRES 10 A 459 ASN SER GLY SER GLU SER VAL ASP THR MET ILE ARG MET SEQRES 11 A 459 VAL ARG ARG TYR TRP ASP VAL GLN GLY LYS PRO GLU LYS SEQRES 12 A 459 LYS THR LEU ILE GLY ARG TRP ASN GLY TYR HIS GLY SER SEQRES 13 A 459 THR ILE GLY GLY ALA SER LEU GLY GLY MET LYS TYR MET SEQRES 14 A 459 HIS GLU GLN GLY ASP LEU PRO ILE PRO GLY MET ALA HIS SEQRES 15 A 459 ILE GLU GLN PRO TRP TRP TYR LYS HIS GLY LYS ASP MET SEQRES 16 A 459 THR PRO ASP GLU PHE GLY VAL VAL ALA ALA ARG TRP LEU SEQRES 17 A 459 GLU GLU LYS ILE LEU GLU ILE GLY ALA ASP LYS VAL ALA SEQRES 18 A 459 ALA PHE VAL GLY GLU PRO ILE GLN GLY ALA GLY GLY VAL SEQRES 19 A 459 ILE VAL PRO PRO ALA THR TYR TRP PRO GLU ILE GLU ARG SEQRES 20 A 459 ILE CYS ARG LYS TYR ASP VAL LEU LEU VAL ALA ASP GLU SEQRES 21 A 459 VAL ILE CYS GLY PHE GLY ARG THR GLY GLU TRP PHE GLY SEQRES 22 A 459 HIS GLN HIS PHE GLY PHE GLN PRO ASP LEU PHE THR ALA SEQRES 23 A 459 ALA LYS GLY LEU SER SER GLY TYR LEU PRO ILE GLY ALA SEQRES 24 A 459 VAL PHE VAL GLY LYS ARG VAL ALA GLU GLY LEU ILE ALA SEQRES 25 A 459 GLY GLY ASP PHE ASN HIS GLY PHE THR TYR SER GLY HIS SEQRES 26 A 459 PRO VAL CYS ALA ALA VAL ALA HIS ALA ASN VAL ALA ALA SEQRES 27 A 459 LEU ARG ASP GLU GLY ILE VAL GLN ARG VAL LYS ASP ASP SEQRES 28 A 459 ILE GLY PRO TYR MET GLN LYS ARG TRP ARG GLU THR PHE SEQRES 29 A 459 SER ARG PHE GLU HIS VAL ASP ASP VAL ARG GLY VAL GLY SEQRES 30 A 459 MET VAL GLN ALA PHE THR LEU VAL LYS ASN LYS ALA LYS SEQRES 31 A 459 ARG GLU LEU PHE PRO ASP PHE GLY GLU ILE GLY THR LEU SEQRES 32 A 459 CYS ARG ASP ILE PHE PHE ARG ASN ASN LEU ILE MET ARG SEQRES 33 A 459 ALA CYS GLY ASP HIS ILE VAL SER ALA PRO PRO LEU VAL SEQRES 34 A 459 MET THR ARG ALA GLU VAL ASP GLU MET LEU ALA VAL ALA SEQRES 35 A 459 GLU ARG CYS LEU GLU GLU PHE GLU GLN THR LEU LYS ALA SEQRES 36 A 459 ARG GLY LEU ALA SEQRES 1 B 459 MET GLN LYS GLN ARG THR THR SER GLN TRP ARG GLU LEU SEQRES 2 B 459 ASP ALA ALA HIS HIS LEU HIS PRO PHE THR ASP THR ALA SEQRES 3 B 459 SER LEU ASN GLN ALA GLY ALA ARG VAL MET THR ARG GLY SEQRES 4 B 459 GLU GLY VAL TYR LEU TRP ASP SER GLU GLY ASN LYS ILE SEQRES 5 B 459 ILE ASP GLY MET ALA GLY LEU TRP CYS VAL ASN VAL GLY SEQRES 6 B 459 TYR GLY ARG LYS ASP PHE ALA GLU ALA ALA ARG ARG GLN SEQRES 7 B 459 MET GLU GLU LEU PRO PHE TYR ASN THR PHE PHE LYS THR SEQRES 8 B 459 THR HIS PRO ALA VAL VAL GLU LEU SER SER LEU LEU ALA SEQRES 9 B 459 GLU VAL THR PRO ALA GLY PHE ASP ARG VAL PHE TYR THR SEQRES 10 B 459 ASN SER GLY SER GLU SER VAL ASP THR MET ILE ARG MET SEQRES 11 B 459 VAL ARG ARG TYR TRP ASP VAL GLN GLY LYS PRO GLU LYS SEQRES 12 B 459 LYS THR LEU ILE GLY ARG TRP ASN GLY TYR HIS GLY SER SEQRES 13 B 459 THR ILE GLY GLY ALA SER LEU GLY GLY MET LYS TYR MET SEQRES 14 B 459 HIS GLU GLN GLY ASP LEU PRO ILE PRO GLY MET ALA HIS SEQRES 15 B 459 ILE GLU GLN PRO TRP TRP TYR LYS HIS GLY LYS ASP MET SEQRES 16 B 459 THR PRO ASP GLU PHE GLY VAL VAL ALA ALA ARG TRP LEU SEQRES 17 B 459 GLU GLU LYS ILE LEU GLU ILE GLY ALA ASP LYS VAL ALA SEQRES 18 B 459 ALA PHE VAL GLY GLU PRO ILE GLN GLY ALA GLY GLY VAL SEQRES 19 B 459 ILE VAL PRO PRO ALA THR TYR TRP PRO GLU ILE GLU ARG SEQRES 20 B 459 ILE CYS ARG LYS TYR ASP VAL LEU LEU VAL ALA ASP GLU SEQRES 21 B 459 VAL ILE CYS GLY PHE GLY ARG THR GLY GLU TRP PHE GLY SEQRES 22 B 459 HIS GLN HIS PHE GLY PHE GLN PRO ASP LEU PHE THR ALA SEQRES 23 B 459 ALA LYS GLY LEU SER SER GLY TYR LEU PRO ILE GLY ALA SEQRES 24 B 459 VAL PHE VAL GLY LYS ARG VAL ALA GLU GLY LEU ILE ALA SEQRES 25 B 459 GLY GLY ASP PHE ASN HIS GLY PHE THR TYR SER GLY HIS SEQRES 26 B 459 PRO VAL CYS ALA ALA VAL ALA HIS ALA ASN VAL ALA ALA SEQRES 27 B 459 LEU ARG ASP GLU GLY ILE VAL GLN ARG VAL LYS ASP ASP SEQRES 28 B 459 ILE GLY PRO TYR MET GLN LYS ARG TRP ARG GLU THR PHE SEQRES 29 B 459 SER ARG PHE GLU HIS VAL ASP ASP VAL ARG GLY VAL GLY SEQRES 30 B 459 MET VAL GLN ALA PHE THR LEU VAL LYS ASN LYS ALA LYS SEQRES 31 B 459 ARG GLU LEU PHE PRO ASP PHE GLY GLU ILE GLY THR LEU SEQRES 32 B 459 CYS ARG ASP ILE PHE PHE ARG ASN ASN LEU ILE MET ARG SEQRES 33 B 459 ALA CYS GLY ASP HIS ILE VAL SER ALA PRO PRO LEU VAL SEQRES 34 B 459 MET THR ARG ALA GLU VAL ASP GLU MET LEU ALA VAL ALA SEQRES 35 B 459 GLU ARG CYS LEU GLU GLU PHE GLU GLN THR LEU LYS ALA SEQRES 36 B 459 ARG GLY LEU ALA HET PXG A 470 25 HET PXG B 470 25 HET SO4 B1460 5 HETNAM PXG 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID HETNAM SO4 SULFATE ION FORMUL 3 PXG 2(C15 H17 N2 O7 P) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *582(H2 O) HELIX 1 1 MET A 56 CYS A 61 5 6 HELIX 2 2 ARG A 68 LEU A 82 1 15 HELIX 3 3 HIS A 93 THR A 107 1 15 HELIX 4 4 SER A 119 GLN A 138 1 20 HELIX 5 5 THR A 157 GLY A 164 1 8 HELIX 6 6 MET A 166 GLN A 172 1 7 HELIX 7 7 TRP A 187 GLY A 192 1 6 HELIX 8 8 THR A 196 GLY A 216 1 21 HELIX 9 9 THR A 240 TYR A 252 1 13 HELIX 10 10 PHE A 272 GLY A 278 1 7 HELIX 11 11 ALA A 287 SER A 292 5 6 HELIX 12 12 GLY A 303 GLY A 313 1 11 HELIX 13 13 PHE A 316 SER A 323 1 8 HELIX 14 14 HIS A 325 GLU A 342 1 18 HELIX 15 15 GLY A 343 ASP A 351 1 9 HELIX 16 16 ASP A 351 SER A 365 1 15 HELIX 17 17 GLY A 398 ASN A 411 1 14 HELIX 18 18 THR A 431 ARG A 456 1 26 HELIX 19 19 MET B 56 CYS B 61 1 6 HELIX 20 20 ARG B 68 LEU B 82 1 15 HELIX 21 21 HIS B 93 THR B 107 1 15 HELIX 22 22 SER B 119 GLN B 138 1 20 HELIX 23 23 THR B 157 GLY B 164 1 8 HELIX 24 24 MET B 166 HIS B 170 5 5 HELIX 25 25 TRP B 187 GLY B 192 1 6 HELIX 26 26 THR B 196 GLY B 216 1 21 HELIX 27 27 THR B 240 TYR B 252 1 13 HELIX 28 28 PHE B 272 GLY B 278 1 7 HELIX 29 29 ALA B 287 SER B 292 5 6 HELIX 30 30 GLY B 303 ALA B 312 1 10 HELIX 31 31 HIS B 325 GLU B 342 1 18 HELIX 32 32 GLY B 343 ASP B 351 1 9 HELIX 33 33 ASP B 351 SER B 365 1 15 HELIX 34 34 GLY B 398 ASN B 411 1 14 HELIX 35 35 THR B 431 ALA B 455 1 25 SHEET 1 AA 4 MET A 36 GLU A 40 0 SHEET 2 AA 4 TYR A 43 ASP A 46 -1 O TYR A 43 N GLU A 40 SHEET 3 AA 4 LYS A 51 ASP A 54 -1 O ILE A 52 N LEU A 44 SHEET 4 AA 4 LEU A 413 ILE A 414 1 N ILE A 414 O ILE A 53 SHEET 1 AB 7 ARG A 113 THR A 117 0 SHEET 2 AB 7 GLY A 298 VAL A 302 -1 O GLY A 298 N THR A 117 SHEET 3 AB 7 LEU A 283 ALA A 286 -1 O PHE A 284 N PHE A 301 SHEET 4 AB 7 LEU A 255 ASP A 259 1 O ALA A 258 N THR A 285 SHEET 5 AB 7 VAL A 220 GLY A 225 1 O ALA A 221 N LEU A 255 SHEET 6 AB 7 THR A 145 ARG A 149 1 O THR A 145 N ALA A 221 SHEET 7 AB 7 MET A 180 ILE A 183 1 O ALA A 181 N GLY A 148 SHEET 1 AC 2 VAL A 370 VAL A 376 0 SHEET 2 AC 2 VAL A 379 ASN A 387 -1 O VAL A 379 N VAL A 376 SHEET 1 AD 2 GLU A 392 LEU A 393 0 SHEET 2 AD 2 VAL A 379 ASN A 387 1 N LYS A 386 O GLU A 392 SHEET 1 AE 4 ARG A 416 CYS A 418 0 SHEET 2 AE 4 HIS A 421 SER A 424 -1 O HIS A 421 N CYS A 418 SHEET 3 AE 4 VAL A 379 ASN A 387 -1 O GLN A 380 N SER A 424 SHEET 4 AE 4 GLU A 392 LEU A 393 1 O GLU A 392 N LYS A 386 SHEET 1 AF 4 ARG A 416 CYS A 418 0 SHEET 2 AF 4 HIS A 421 SER A 424 -1 O HIS A 421 N CYS A 418 SHEET 3 AF 4 VAL A 379 ASN A 387 -1 O GLN A 380 N SER A 424 SHEET 4 AF 4 VAL A 370 VAL A 376 -1 O ASP A 371 N THR A 383 SHEET 1 BA 4 MET B 36 GLU B 40 0 SHEET 2 BA 4 TYR B 43 ASP B 46 -1 O TYR B 43 N GLU B 40 SHEET 3 BA 4 LYS B 51 ASP B 54 -1 O ILE B 52 N LEU B 44 SHEET 4 BA 4 LEU B 413 ILE B 414 1 N ILE B 414 O ILE B 53 SHEET 1 BB 2 THR B 87 PHE B 88 0 SHEET 2 BB 2 THR B 91 THR B 92 -1 O THR B 91 N PHE B 88 SHEET 1 BC 7 ARG B 113 THR B 117 0 SHEET 2 BC 7 GLY B 298 VAL B 302 -1 O GLY B 298 N THR B 117 SHEET 3 BC 7 LEU B 283 ALA B 286 -1 O PHE B 284 N PHE B 301 SHEET 4 BC 7 LEU B 255 ASP B 259 1 O ALA B 258 N THR B 285 SHEET 5 BC 7 VAL B 220 GLY B 225 1 O ALA B 221 N LEU B 255 SHEET 6 BC 7 THR B 145 ARG B 149 1 O THR B 145 N ALA B 221 SHEET 7 BC 7 MET B 180 ILE B 183 1 O ALA B 181 N GLY B 148 SHEET 1 BD 2 VAL B 370 VAL B 376 0 SHEET 2 BD 2 VAL B 379 ASN B 387 -1 O VAL B 379 N VAL B 376 SHEET 1 BE 2 GLU B 392 LEU B 393 0 SHEET 2 BE 2 VAL B 379 ASN B 387 1 N LYS B 386 O GLU B 392 SHEET 1 BF 4 ARG B 416 CYS B 418 0 SHEET 2 BF 4 HIS B 421 SER B 424 -1 O HIS B 421 N CYS B 418 SHEET 3 BF 4 VAL B 379 ASN B 387 -1 O GLN B 380 N SER B 424 SHEET 4 BF 4 GLU B 392 LEU B 393 1 O GLU B 392 N ASN B 387 SHEET 1 BG 4 ARG B 416 CYS B 418 0 SHEET 2 BG 4 HIS B 421 SER B 424 -1 O HIS B 421 N CYS B 418 SHEET 3 BG 4 VAL B 379 ASN B 387 -1 O GLN B 380 N SER B 424 SHEET 4 BG 4 VAL B 370 VAL B 376 -1 O ASP B 371 N THR B 383 CISPEP 1 LEU A 175 PRO A 176 0 0.59 CISPEP 2 LEU B 175 PRO B 176 0 -3.92 SITE 1 AC1 22 LEU A 59 TRP A 60 SER A 119 GLY A 120 SITE 2 AC1 22 SER A 121 TYR A 153 HIS A 154 GLY A 155 SITE 3 AC1 22 GLU A 226 ALA A 231 ASP A 259 VAL A 261 SITE 4 AC1 22 ILE A 262 ALA A 287 ARG A 416 HOH A2025 SITE 5 AC1 22 HOH A2193 HOH A2233 HOH A2235 HOH A2305 SITE 6 AC1 22 HOH A2306 HOH A2307 SITE 1 AC2 21 HOH A2091 LEU B 59 TRP B 60 SER B 119 SITE 2 AC2 21 GLY B 120 SER B 121 TYR B 153 HIS B 154 SITE 3 AC2 21 GLY B 155 GLU B 226 ALA B 231 ASP B 259 SITE 4 AC2 21 VAL B 261 ILE B 262 ALA B 287 ARG B 416 SITE 5 AC2 21 HOH B2075 HOH B2076 HOH B2161 HOH B2272 SITE 6 AC2 21 HOH B2273 SITE 1 AC3 4 ASN A 387 THR B 196 PRO B 197 ASP B 198 CRYST1 58.452 60.536 61.300 68.40 76.18 84.28 P 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 0.017108 -0.001714 -0.003851 0.00000 SCALE2 0.000000 0.016602 -0.006332 0.00000 SCALE3 0.000000 0.000000 0.017980 0.00000