HEADER TRANSFERASE 08-NOV-11 4A6R TITLE CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM TITLE 2 VIOLACEUM IN THE APO FORM, CRYSTALLISED FROM POLYACRYLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: OMEGA TRANSAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PROBABLE AMINOTRANSFERASE; COMPND 5 EC: 2.6.1.18, 2.6.1.62; COMPND 6 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: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS TRANSFERASE, PLP-BINDING ENZYME, TRANSAMINASE FOLD TYPE I EXPDTA X-RAY DIFFRACTION AUTHOR D.T.LOGAN,M.HAKANSSON,K.YENGO,M.SVEDENDAHL HUMBLE,K.ENGELMARK AUTHOR 2 CASSIMJEE,B.WALSE,V.ABEDI,H.-J.FEDERSEL,P.BERGLUND REVDAT 4 20-DEC-23 4A6R 1 REMARK REVDAT 3 17-JAN-18 4A6R 1 REMARK REVDAT 2 01-AUG-12 4A6R 1 JRNL REVDAT 1 25-JAN-12 4A6R 0 JRNL AUTH M.SVEDENDAHL HUMBLE,K.ENGELMARK CASSIMJEE,M.HAKANSSON, JRNL AUTH 2 Y.R.KIMBUNG,B.WALSE,V.ABEDI,H.-J.FEDERSEL,P.BERGLUND, JRNL AUTH 3 D.T.LOGAN JRNL TITL CRYSTAL STRUCTURES OF THE CHROMOBACTERIUM VIOLACEUM JRNL TITL 2 OMEGA-TRANSAMINASE REVEAL MAJOR STRUCTURAL REARRANGEMENTS JRNL TITL 3 UPON BINDING OF COENZYME PLP. JRNL REF FEBS J. V. 279 779 2012 JRNL REFN ISSN 1742-464X JRNL PMID 22268978 JRNL DOI 10.1111/J.1742-4658.2011.08468.X REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 169719 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.135 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 8516 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.2900 - 4.1838 0.97 5537 307 0.1487 0.1427 REMARK 3 2 4.1838 - 3.3239 0.98 5542 323 0.1367 0.1500 REMARK 3 3 3.3239 - 2.9046 0.98 5590 274 0.1421 0.1659 REMARK 3 4 2.9046 - 2.6394 0.97 5550 284 0.1345 0.1657 REMARK 3 5 2.6394 - 2.4505 0.97 5512 291 0.1223 0.1376 REMARK 3 6 2.4505 - 2.3061 0.96 5523 284 0.1156 0.1431 REMARK 3 7 2.3061 - 2.1907 0.96 5521 262 0.1108 0.1430 REMARK 3 8 2.1907 - 2.0954 0.96 5514 275 0.1140 0.1507 REMARK 3 9 2.0954 - 2.0148 0.96 5477 282 0.1155 0.1598 REMARK 3 10 2.0148 - 1.9453 0.95 5408 285 0.1155 0.1549 REMARK 3 11 1.9453 - 1.8845 0.95 5436 285 0.1125 0.1489 REMARK 3 12 1.8845 - 1.8307 0.95 5399 299 0.1106 0.1362 REMARK 3 13 1.8307 - 1.7825 0.94 5401 271 0.1043 0.1422 REMARK 3 14 1.7825 - 1.7390 0.95 5458 278 0.1089 0.1557 REMARK 3 15 1.7390 - 1.6995 0.94 5339 310 0.1146 0.1632 REMARK 3 16 1.6995 - 1.6633 0.94 5345 302 0.1143 0.1725 REMARK 3 17 1.6633 - 1.6301 0.94 5322 294 0.1146 0.1615 REMARK 3 18 1.6301 - 1.5993 0.93 5356 287 0.1132 0.1563 REMARK 3 19 1.5993 - 1.5708 0.94 5360 273 0.1214 0.1572 REMARK 3 20 1.5708 - 1.5442 0.94 5276 287 0.1278 0.1719 REMARK 3 21 1.5442 - 1.5193 0.93 5304 293 0.1345 0.1757 REMARK 3 22 1.5193 - 1.4959 0.93 5315 261 0.1433 0.1956 REMARK 3 23 1.4959 - 1.4739 0.92 5198 288 0.1520 0.1890 REMARK 3 24 1.4739 - 1.4531 0.92 5375 264 0.1654 0.2118 REMARK 3 25 1.4531 - 1.4335 0.92 5246 285 0.1820 0.2416 REMARK 3 26 1.4335 - 1.4149 0.92 5243 280 0.1886 0.2215 REMARK 3 27 1.4149 - 1.3972 0.92 5279 278 0.1936 0.2684 REMARK 3 28 1.3972 - 1.3804 0.91 5151 274 0.2079 0.2509 REMARK 3 29 1.3804 - 1.3643 0.92 5269 273 0.2212 0.2646 REMARK 3 30 1.3643 - 1.3490 0.86 4957 267 0.2994 0.3518 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 44.04 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99410 REMARK 3 B22 (A**2) : 0.08580 REMARK 3 B33 (A**2) : 0.90820 REMARK 3 B12 (A**2) : 0.77650 REMARK 3 B13 (A**2) : 0.27330 REMARK 3 B23 (A**2) : 0.47370 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 6924 REMARK 3 ANGLE : 1.219 9386 REMARK 3 CHIRALITY : 0.071 984 REMARK 3 PLANARITY : 0.007 1232 REMARK 3 DIHEDRAL : 13.098 2522 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4A6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1290050224. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0397 REMARK 200 MONOCHROMATOR : BENT SI (111) CRYSTAL, REMARK 200 HORIZONTALLY FOCUSING REMARK 200 OPTICS : MULTILAYER MIRROR, VERTICALLY REMARK 200 FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH SX-165 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 690977 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3HMU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 0.1 M HEPES PH 7.5, 22% REMARK 280 W/V POLYACRYLIC ACID 5100 SODIUM SALT, PH 7.4 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: 4980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 ALA A 33 REMARK 465 GLU A 171 REMARK 465 GLN A 172 REMARK 465 GLY A 173 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 465 ALA B 33 REMARK 465 GLU B 171 REMARK 465 GLN B 172 REMARK 465 GLY B 173 REMARK 465 ASP B 174 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 2278 O HOH A 2288 1.61 REMARK 500 OE2 GLU B 244 O HOH B 2197 1.83 REMARK 500 O HOH B 2003 O HOH B 2005 1.85 REMARK 500 O HOH A 2126 O HOH A 2264 1.97 REMARK 500 O HOH B 2270 O HOH B 2273 2.10 REMARK 500 O HOH A 2010 O HOH B 2020 2.11 REMARK 500 O HOH A 2142 O HOH A 2290 2.16 REMARK 500 O HOH B 2093 O HOH B 2283 2.17 REMARK 500 O HOH B 2248 O HOH B 2249 2.17 REMARK 500 OD2 ASP B 125 NH1 ARG B 129 2.18 REMARK 500 O HOH A 2010 O HOH B 2046 2.18 REMARK 500 OD1 ASP A 253 O HOH A 2287 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2275 O HOH B 2238 1455 1.96 REMARK 500 O HOH A 2371 O HOH B 2324 1444 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG B 38 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LEU B 283 CA - CB - CG ANGL. DEV. = 14.3 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 LEU A 82 79.58 -166.69 REMARK 500 LYS A 193 -129.40 53.76 REMARK 500 ALA A 287 -154.11 -122.11 REMARK 500 ASP A 351 -75.85 -135.30 REMARK 500 PHE A 397 117.88 -35.52 REMARK 500 ALA A 425 75.60 -156.90 REMARK 500 LEU B 82 79.90 -167.81 REMARK 500 LYS B 193 -127.21 52.70 REMARK 500 ALA B 287 -158.73 -123.02 REMARK 500 ASP B 351 -77.02 -136.87 REMARK 500 PHE B 397 118.79 -36.37 REMARK 500 ALA B 425 76.69 -154.83 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 A2098 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A2192 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH B2157 DISTANCE = 6.00 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 POLYACRYLIC ACID (TA8): POLYACRYLIC ACID (N=3) REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TA8 A 1460 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TA8 B 1460 REMARK 900 REMARK 900 RELATED ENTRIES 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 DBREF 4A6R A 1 459 UNP Q7NWG4 Q7NWG4_CHRVO 1 459 DBREF 4A6R 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 TA8 A1460 20 HET TA8 B1460 20 HETNAM TA8 POLYACRYLIC ACID HETSYN TA8 OCTANE-1,3,5,7-TETRACARBOXYLIC ACID FORMUL 3 TA8 2(C12 H18 O8) FORMUL 5 HOH *842(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 TRP A 187 GLY A 192 1 6 HELIX 7 7 THR A 196 GLY A 216 1 21 HELIX 8 8 THR A 240 TYR A 252 1 13 HELIX 9 9 PHE A 272 GLY A 278 1 7 HELIX 10 10 ALA A 287 SER A 292 5 6 HELIX 11 11 GLY A 303 GLY A 314 1 12 HELIX 12 12 PHE A 316 SER A 323 1 8 HELIX 13 13 HIS A 325 GLU A 342 1 18 HELIX 14 14 GLY A 343 ASP A 351 1 9 HELIX 15 15 ASP A 351 SER A 365 1 15 HELIX 16 16 GLY A 398 ASN A 411 1 14 HELIX 17 17 THR A 431 ARG A 456 1 26 HELIX 18 18 MET B 56 CYS B 61 1 6 HELIX 19 19 ARG B 68 LEU B 82 1 15 HELIX 20 20 HIS B 93 THR B 107 1 15 HELIX 21 21 SER B 119 GLN B 138 1 20 HELIX 22 22 THR B 157 GLY B 164 1 8 HELIX 23 23 TRP B 187 GLY B 192 1 6 HELIX 24 24 THR B 196 GLY B 216 1 21 HELIX 25 25 THR B 240 TYR B 252 1 13 HELIX 26 26 PHE B 272 GLY B 278 1 7 HELIX 27 27 ALA B 287 SER B 292 5 6 HELIX 28 28 GLY B 303 GLY B 314 1 12 HELIX 29 29 PHE B 316 SER B 323 1 8 HELIX 30 30 HIS B 325 GLU B 342 1 18 HELIX 31 31 GLY B 343 ASP B 351 1 9 HELIX 32 32 ASP B 351 SER B 365 1 15 HELIX 33 33 GLY B 398 ASN B 411 1 14 HELIX 34 34 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 4 VAL A 370 VAL A 376 0 SHEET 2 AC 4 VAL A 379 LEU A 384 -1 O VAL A 379 N VAL A 376 SHEET 3 AC 4 HIS A 421 SER A 424 -1 O ILE A 422 N PHE A 382 SHEET 4 AC 4 ARG A 416 CYS A 418 -1 O ARG A 416 N VAL A 423 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 -0.15 CISPEP 2 LEU B 175 PRO B 176 0 2.82 SITE 1 AC1 14 SER A 119 GLY A 120 SER A 121 TYR A 153 SITE 2 AC1 14 SER A 156 THR A 157 HOH A2140 HOH A2141 SITE 3 AC1 14 HOH A2438 THR B 117 ASN B 118 GLU B 122 SITE 4 AC1 14 THR B 126 ARG B 129 SITE 1 AC2 15 THR A 117 ASN A 118 GLU A 122 THR A 126 SITE 2 AC2 15 ARG A 129 HOH A2123 HOH A2132 SER B 119 SITE 3 AC2 15 GLY B 120 SER B 121 TYR B 153 SER B 156 SITE 4 AC2 15 THR B 157 HOH B2100 HOH B2404 CRYST1 58.590 61.870 63.540 108.03 87.31 105.16 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 0.017068 0.004624 0.000656 0.00000 SCALE2 0.000000 0.016746 0.005427 0.00000 SCALE3 0.000000 0.000000 0.016562 0.00000 MTRIX1 1 -0.997200 -0.057090 0.048490 65.81000 1 MTRIX2 1 -0.068420 0.430900 -0.899800 34.71000 1 MTRIX3 1 0.030470 -0.900600 -0.433600 50.55000 1