HEADER TRANSFERASE 11-SEP-12 4BA4 TITLE CRYSTAL STRUCTURE OF THE APO OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM TITLE 2 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 4 20-DEC-23 4BA4 1 REMARK REVDAT 3 15-MAY-13 4BA4 1 MTRIX1 MTRIX2 MTRIX3 REVDAT 2 03-APR-13 4BA4 1 JRNL REVDAT 1 27-MAR-13 4BA4 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. 1.73 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.6 REMARK 3 NUMBER OF REFLECTIONS : 74538 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3933 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) : 1.73 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5192 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.3220 REMARK 3 BIN FREE R VALUE SET COUNT : 278 REMARK 3 BIN FREE R VALUE : 0.3660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 875 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.09000 REMARK 3 B22 (A**2) : -1.09000 REMARK 3 B33 (A**2) : 0.31000 REMARK 3 B12 (A**2) : 0.58000 REMARK 3 B13 (A**2) : -0.92000 REMARK 3 B23 (A**2) : 1.05000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.129 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.391 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7252 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9875 ; 1.243 ; 1.946 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 956 ; 5.537 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 353 ;32.693 ;23.031 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1258 ;14.949 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 64 ;17.083 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1027 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5680 ; 0.006 ; 0.021 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 : 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 4BA4 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_1290054041. 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) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 14.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.1000 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 (%) : 81.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 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 1QJ3 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: 5540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.1 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 167 CG CD CE NZ 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. = 15.3 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 TRP A 60 27.07 49.98 REMARK 500 LEU A 82 84.77 -161.61 REMARK 500 LYS A 193 -125.08 48.88 REMARK 500 ALA A 287 -158.19 -113.99 REMARK 500 ASP A 351 -80.77 -131.35 REMARK 500 PHE A 397 118.86 -34.16 REMARK 500 ALA A 425 73.51 -153.12 REMARK 500 LEU B 82 83.61 -168.50 REMARK 500 GLN B 172 47.06 -86.90 REMARK 500 ASP B 174 55.69 -119.47 REMARK 500 LYS B 193 -125.24 51.70 REMARK 500 ALA B 287 -157.36 -120.26 REMARK 500 ASP B 351 -84.08 -131.40 REMARK 500 PHE B 397 115.07 -32.88 REMARK 500 ALA B 425 74.95 -154.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2033 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A2112 DISTANCE = 6.83 ANGSTROMS REMARK 525 HOH A2115 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2225 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A2226 DISTANCE = 6.39 ANGSTROMS REMARK 525 HOH A2241 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B2027 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B2092 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH B2107 DISTANCE = 5.82 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 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: 4BA5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM REMARK 900 VIOLACEUM DBREF 4BA4 A 1 459 UNP Q7NWG4 Q7NWG4_CHRVO 1 459 DBREF 4BA4 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 SO4 B1460 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *875(H2 O) HELIX 1 1 MET A 56 CYS A 61 1 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 ASP A 253 1 14 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 314 1 12 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 GLN B 172 1 7 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 ASP B 253 1 14 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 GLY B 314 1 12 HELIX 31 31 PHE B 316 SER B 323 1 8 HELIX 32 32 HIS B 325 GLU B 342 1 18 HELIX 33 33 GLY B 343 ASP B 351 1 9 HELIX 34 34 ASP B 351 SER B 365 1 15 HELIX 35 35 GLY B 398 ASN B 411 1 14 HELIX 36 36 THR B 431 ARG B 456 1 26 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 7 ARG B 113 THR B 117 0 SHEET 2 BB 7 GLY B 298 VAL B 302 -1 O GLY B 298 N THR B 117 SHEET 3 BB 7 LEU B 283 ALA B 286 -1 O PHE B 284 N PHE B 301 SHEET 4 BB 7 LEU B 255 ASP B 259 1 O ALA B 258 N THR B 285 SHEET 5 BB 7 VAL B 220 GLY B 225 1 O ALA B 221 N LEU B 255 SHEET 6 BB 7 THR B 145 ARG B 149 1 O THR B 145 N ALA B 221 SHEET 7 BB 7 MET B 180 ILE B 183 1 O ALA B 181 N GLY B 148 SHEET 1 BC 4 VAL B 370 VAL B 376 0 SHEET 2 BC 4 VAL B 379 LEU B 384 -1 O VAL B 379 N VAL B 376 SHEET 3 BC 4 HIS B 421 SER B 424 -1 O ILE B 422 N PHE B 382 SHEET 4 BC 4 ARG B 416 CYS B 418 -1 O ARG B 416 N VAL B 423 CISPEP 1 LEU A 175 PRO A 176 0 -0.47 CISPEP 2 LEU B 175 PRO B 176 0 1.03 SITE 1 AC1 6 ARG B 347 THR B 431 ARG B 432 HOH B2318 SITE 2 AC1 6 HOH B2377 HOH B2383 CRYST1 58.837 61.897 63.907 71.91 86.99 74.58 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 0.016996 -0.004688 0.000579 0.00000 SCALE2 0.000000 0.016759 -0.005426 0.00000 SCALE3 0.000000 0.000000 0.016470 0.00000 MTRIX1 1 -0.998000 0.062000 0.023000 25.40965 1 MTRIX2 1 0.047000 0.430000 0.902000 -12.99831 1 MTRIX3 1 0.046000 0.901000 -0.432000 19.02801 1