HEADER TRANSFERASE 10-MAY-13 4KNZ OBSLTE 30-JAN-19 4KNZ 6NNR TITLE THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CB3717 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TS, TSASE; COMPND 5 EC: 2.1.1.45; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B2827, JW2795, THYA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ALPHA/BETA PROTEIN, METHYLTRANSFERASE, METHYLENETETRAHYDROFOLATE, KEYWDS 2 ANTIFOLATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.NEWBY,T.T.LEE,J.FINER-MOORE,R.M.STROUD REVDAT 4 30-JAN-19 4KNZ 1 OBSLTE REVDAT 3 15-NOV-17 4KNZ 1 REMARK REVDAT 2 05-JUN-13 4KNZ 1 JRNL REVDAT 1 22-MAY-13 4KNZ 0 SPRSDE 22-MAY-13 4KNZ 4IW5 JRNL AUTH Z.WANG,P.J.SAPIENZA,T.ABEYSINGHE,C.LUZUM,A.L.LEE, JRNL AUTH 2 J.S.FINER-MOORE,R.M.STROUD,A.KOHEN JRNL TITL MG(2+) BINDS TO THE SURFACE OF THYMIDYLATE SYNTHASE AND JRNL TITL 2 AFFECTS HYDRIDE TRANSFER AT THE INTERIOR ACTIVE SITE. JRNL REF J.AM.CHEM.SOC. V. 135 7583 2013 JRNL REFN ISSN 0002-7863 JRNL PMID 23611499 JRNL DOI 10.1021/JA400761X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.NEWBY,T.T.LEE,R.J.MORSE,Y.LIU,L.LIU,P.VENKATRAMAN, REMARK 1 AUTH 2 D.V.SANTI,J.S.FINER-MOORE,R.M.STROUD REMARK 1 TITL THE ROLE OF PROTEIN DYNAMICS IN THYMIDYLATE SYNTHASE REMARK 1 TITL 2 CATALYSIS: VARIANTS OF CONSERVED 2'-DEOXYURIDINE REMARK 1 TITL 3 5'-MONOPHOSPHATE (DUMP)-BINDING TYR-261. REMARK 1 REF BIOCHEMISTRY V. 45 7415 2006 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 16768437 REMARK 1 DOI 10.1021/BI060152S REMARK 1 REFERENCE 2 REMARK 1 AUTH Z.WANG,T.ABEYSINGHE,J.S.FINER-MOORE,R.M.STROUD,A.KOHEN REMARK 1 TITL A REMOTE MUTATION AFFECTS THE HYDRIDE TRANSFER BY DISRUPTING REMARK 1 TITL 2 CONCERTED PROTEIN MOTIONS IN THYMIDYLATE SYNTHASE. REMARK 1 REF J.AM.CHEM.SOC. V. 134 17722 2012 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 23034004 REMARK 1 DOI 10.1021/JA307859M REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 141141 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.154 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 14035 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 45.6757 - 4.0385 0.99 4512 458 0.1538 0.1553 REMARK 3 2 4.0385 - 3.2057 1.00 4422 497 0.1252 0.1380 REMARK 3 3 3.2057 - 2.8006 1.00 4410 503 0.1416 0.1539 REMARK 3 4 2.8006 - 2.5445 1.00 4370 495 0.1394 0.1635 REMARK 3 5 2.5445 - 2.3622 0.99 4400 473 0.1325 0.1580 REMARK 3 6 2.3622 - 2.2229 0.99 4354 503 0.1215 0.1425 REMARK 3 7 2.2229 - 2.1116 1.00 4407 481 0.1234 0.1541 REMARK 3 8 2.1116 - 2.0197 0.99 4353 463 0.1294 0.1494 REMARK 3 9 2.0197 - 1.9419 0.99 4358 476 0.1263 0.1511 REMARK 3 10 1.9419 - 1.8749 0.99 4356 477 0.1202 0.1473 REMARK 3 11 1.8749 - 1.8163 0.99 4323 491 0.1186 0.1504 REMARK 3 12 1.8163 - 1.7644 0.98 4280 506 0.1151 0.1491 REMARK 3 13 1.7644 - 1.7179 0.98 4336 466 0.1171 0.1523 REMARK 3 14 1.7179 - 1.6760 0.98 4263 469 0.1140 0.1561 REMARK 3 15 1.6760 - 1.6379 0.98 4307 513 0.1104 0.1521 REMARK 3 16 1.6379 - 1.6030 0.98 4272 433 0.1087 0.1486 REMARK 3 17 1.6030 - 1.5710 0.97 4296 472 0.1083 0.1384 REMARK 3 18 1.5710 - 1.5413 0.97 4193 472 0.1050 0.1496 REMARK 3 19 1.5413 - 1.5138 0.97 4243 463 0.1042 0.1425 REMARK 3 20 1.5138 - 1.4881 0.96 4215 458 0.1064 0.1445 REMARK 3 21 1.4881 - 1.4641 0.96 4165 471 0.1125 0.1570 REMARK 3 22 1.4641 - 1.4416 0.95 4149 448 0.1152 0.1550 REMARK 3 23 1.4416 - 1.4204 0.94 4137 454 0.1197 0.1685 REMARK 3 24 1.4204 - 1.4004 0.94 4103 498 0.1330 0.1778 REMARK 3 25 1.4004 - 1.3815 0.93 4067 427 0.1369 0.1851 REMARK 3 26 1.3815 - 1.3635 0.93 4028 442 0.1443 0.1728 REMARK 3 27 1.3635 - 1.3465 0.92 4069 432 0.1567 0.2092 REMARK 3 28 1.3465 - 1.3302 0.91 3983 428 0.1667 0.2094 REMARK 3 29 1.3302 - 1.3148 0.89 3895 426 0.1857 0.2305 REMARK 3 30 1.3148 - 1.3000 0.88 3840 440 0.2034 0.2414 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.47 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 50.44 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 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 : 0.009 4645 REMARK 3 ANGLE : 1.365 6328 REMARK 3 CHIRALITY : 0.080 661 REMARK 3 PLANARITY : 0.008 820 REMARK 3 DIHEDRAL : 16.241 1724 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 4KNZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-FEB-04 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115869 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : MONOCHROMETER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 146174 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.648 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.60800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 2TSC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.2MG/ML PROTEIN, 17MM KPO4, 3.3MM REMARK 280 DUMP, 3.3MM CB3717, 3.3MM DTT, AND EITHER 0.5% ETHYL ACETATE OR REMARK 280 4% N-PROPANOL AGAINST 1.4M NA CITRATE, PH 7.4, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.29000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 33.29000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.29000 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: 6560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 636 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 751 LIES ON A SPECIAL POSITION. 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 THR A 103 H GLY A 106 1.48 REMARK 500 O HOH A 1300 O HOH A 1430 1.94 REMARK 500 O HOH A 1202 O HOH A 1331 1.95 REMARK 500 SG CYS A 50 O HOH A 1323 1.97 REMARK 500 O HOH A 1177 O HOH A 1331 2.01 REMARK 500 O HOH A 1465 O HOH A 1466 2.02 REMARK 500 O HOH B 660 O HOH B 750 2.05 REMARK 500 NE2 GLN A 64 O HOH A 1338 2.07 REMARK 500 O HOH A 1193 O HOH A 1450 2.07 REMARK 500 O HOH A 1314 O HOH A 1433 2.08 REMARK 500 O HIS B 108 O HOH B 646 2.08 REMARK 500 O HOH A 1279 O HOH A 1395 2.10 REMARK 500 O HOH A 1431 O HOH A 1439 2.13 REMARK 500 O HOH A 1247 O HOH A 1456 2.15 REMARK 500 OD2 ASP B 139 O HOH B 749 2.16 REMARK 500 O HOH A 1249 O HOH A 1430 2.16 REMARK 500 O HOH B 485 O HOH B 628 2.17 REMARK 500 O HOH B 759 O HOH B 760 2.17 REMARK 500 O PRO A 102 O HOH A 1324 2.18 REMARK 500 O HOH B 443 O HOH B 628 2.18 REMARK 500 OG1 THR B 103 OD2 ASP B 105 2.18 REMARK 500 O HOH A 1298 O HOH A 1345 2.19 REMARK 500 O HOH B 496 O HOH B 744 2.19 REMARK 500 O HOH A 1226 O HOH A 1302 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 1369 O HOH B 701 6544 2.14 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 100 58.11 -160.50 REMARK 500 PRO A 104 -16.79 -34.39 REMARK 500 ASP A 122 63.03 -152.95 REMARK 500 VAL B 93 -159.24 -85.77 REMARK 500 ALA B 100 52.65 -154.21 REMARK 500 ASP B 122 59.72 -143.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 903 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 76 O REMARK 620 2 HOH A1464 O 99.2 REMARK 620 3 HOH A1298 O 89.9 170.9 REMARK 620 4 HOH A1465 O 99.7 85.8 92.2 REMARK 620 5 HOH A1317 O 168.1 83.1 87.9 68.7 REMARK 620 6 HOH A1054 O 102.4 90.6 87.9 157.9 89.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMC A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CB3 A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMC B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CB3 B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GEV RELATED DB: PDB REMARK 900 E. COLI Y209W THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND REMARK 900 CB3717 DBREF 4KNZ A 1 264 UNP P0A884 TYSY_ECOLI 1 264 DBREF 4KNZ B 1 264 UNP P0A884 TYSY_ECOLI 1 264 SEQRES 1 A 264 CXM LYS GLN TYR LEU GLU LEU MET GLN LYS VAL LEU ASP SEQRES 2 A 264 GLU GLY THR GLN LYS ASN ASP ARG THR GLY THR GLY THR SEQRES 3 A 264 LEU SER ILE PHE GLY HIS GLN MET ARG PHE ASN LEU GLN SEQRES 4 A 264 ASP GLY PHE PRO LEU VAL THR THR LYS ARG CYS HIS LEU SEQRES 5 A 264 ARG SER ILE ILE HIS GLU LEU LEU TRP PHE LEU GLN GLY SEQRES 6 A 264 ASP THR ASN ILE ALA TYR LEU HIS GLU ASN ASN VAL THR SEQRES 7 A 264 ILE TRP ASP GLU TRP ALA ASP GLU ASN GLY ASP LEU GLY SEQRES 8 A 264 PRO VAL TYR GLY LYS GLN TRP ARG ALA TRP PRO THR PRO SEQRES 9 A 264 ASP GLY ARG HIS ILE ASP GLN ILE THR THR VAL LEU ASN SEQRES 10 A 264 GLN LEU LYS ASN ASP PRO ASP SER ARG ARG ILE ILE VAL SEQRES 11 A 264 SER ALA TRP ASN VAL GLY GLU LEU ASP LYS MET ALA LEU SEQRES 12 A 264 ALA PRO CYS HIS ALA PHE PHE GLN PHE TYR VAL ALA ASP SEQRES 13 A 264 GLY LYS LEU SER CYS GLN LEU TYR GLN ARG SER CYS ASP SEQRES 14 A 264 VAL PHE LEU GLY LEU PRO PHE ASN ILE ALA SER TYR ALA SEQRES 15 A 264 LEU LEU VAL HIS MET MET ALA GLN GLN CYS ASP LEU GLU SEQRES 16 A 264 VAL GLY ASP PHE VAL TRP THR GLY GLY ASP THR HIS LEU SEQRES 17 A 264 TYR SER ASN HIS MET ASP GLN THR HIS LEU GLN LEU SER SEQRES 18 A 264 ARG GLU PRO ARG PRO LEU PRO LYS LEU ILE ILE LYS ARG SEQRES 19 A 264 LYS PRO GLU SER ILE PHE ASP TYR ARG PHE GLU ASP PHE SEQRES 20 A 264 GLU ILE GLU GLY TYR ASP PRO HIS PRO GLY ILE LYS ALA SEQRES 21 A 264 PRO VAL ALA ILE SEQRES 1 B 264 CXM LYS GLN TYR LEU GLU LEU MET GLN LYS VAL LEU ASP SEQRES 2 B 264 GLU GLY THR GLN LYS ASN ASP ARG THR GLY THR GLY THR SEQRES 3 B 264 LEU SER ILE PHE GLY HIS GLN MET ARG PHE ASN LEU GLN SEQRES 4 B 264 ASP GLY PHE PRO LEU VAL THR THR LYS ARG CYS HIS LEU SEQRES 5 B 264 ARG SER ILE ILE HIS GLU LEU LEU TRP PHE LEU GLN GLY SEQRES 6 B 264 ASP THR ASN ILE ALA TYR LEU HIS GLU ASN ASN VAL THR SEQRES 7 B 264 ILE TRP ASP GLU TRP ALA ASP GLU ASN GLY ASP LEU GLY SEQRES 8 B 264 PRO VAL TYR GLY LYS GLN TRP ARG ALA TRP PRO THR PRO SEQRES 9 B 264 ASP GLY ARG HIS ILE ASP GLN ILE THR THR VAL LEU ASN SEQRES 10 B 264 GLN LEU LYS ASN ASP PRO ASP SER ARG ARG ILE ILE VAL SEQRES 11 B 264 SER ALA TRP ASN VAL GLY GLU LEU ASP LYS MET ALA LEU SEQRES 12 B 264 ALA PRO CYS HIS ALA PHE PHE GLN PHE TYR VAL ALA ASP SEQRES 13 B 264 GLY LYS LEU SER CYS GLN LEU TYR GLN ARG SER CYS ASP SEQRES 14 B 264 VAL PHE LEU GLY LEU PRO PHE ASN ILE ALA SER TYR ALA SEQRES 15 B 264 LEU LEU VAL HIS MET MET ALA GLN GLN CYS ASP LEU GLU SEQRES 16 B 264 VAL GLY ASP PHE VAL TRP THR GLY GLY ASP THR HIS LEU SEQRES 17 B 264 TYR SER ASN HIS MET ASP GLN THR HIS LEU GLN LEU SER SEQRES 18 B 264 ARG GLU PRO ARG PRO LEU PRO LYS LEU ILE ILE LYS ARG SEQRES 19 B 264 LYS PRO GLU SER ILE PHE ASP TYR ARG PHE GLU ASP PHE SEQRES 20 B 264 GLU ILE GLU GLY TYR ASP PRO HIS PRO GLY ILE LYS ALA SEQRES 21 B 264 PRO VAL ALA ILE MODRES 4KNZ CXM A 1 MET N-CARBOXYMETHIONINE MODRES 4KNZ CXM B 1 MET N-CARBOXYMETHIONINE HET CXM A 1 18 HET CXM B 1 18 HET UMC A 901 20 HET CB3 A 902 56 HET NA A 903 1 HET UMC B 301 20 HET CB3 B 302 56 HETNAM CXM N-CARBOXYMETHIONINE HETNAM UMC 2'-DEOXY-5'-URIDYLIC ACID HETNAM CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID HETNAM NA SODIUM ION FORMUL 1 CXM 2(C6 H11 N O4 S) FORMUL 3 UMC 2(C9 H15 N2 O8 P) FORMUL 4 CB3 2(C24 H23 N5 O6) FORMUL 5 NA NA 1+ FORMUL 8 HOH *837(H2 O) HELIX 1 1 CXM A 1 GLY A 15 1 15 HELIX 2 2 GLN A 39 GLY A 41 5 3 HELIX 3 3 HIS A 51 GLY A 65 1 15 HELIX 4 4 ILE A 69 ASN A 75 1 7 HELIX 5 5 TRP A 80 ALA A 84 5 5 HELIX 6 6 VAL A 93 ALA A 100 1 8 HELIX 7 7 ASP A 110 ASP A 122 1 13 HELIX 8 8 ASN A 134 MET A 141 5 8 HELIX 9 9 LEU A 172 ASP A 193 1 22 HELIX 10 10 HIS A 212 SER A 221 1 10 HELIX 11 11 ARG A 243 GLU A 245 5 3 HELIX 12 12 LYS B 2 GLY B 15 1 14 HELIX 13 13 GLN B 39 GLY B 41 5 3 HELIX 14 14 HIS B 51 GLN B 64 1 14 HELIX 15 15 ILE B 69 ASN B 75 1 7 HELIX 16 16 TRP B 80 ALA B 84 5 5 HELIX 17 17 VAL B 93 ALA B 100 1 8 HELIX 18 18 ASP B 110 ASP B 122 1 13 HELIX 19 19 ASN B 134 MET B 141 5 8 HELIX 20 20 LEU B 172 CYS B 192 1 21 HELIX 21 21 HIS B 212 SER B 221 1 10 HELIX 22 22 ARG B 243 GLU B 245 5 3 SHEET 1 A 6 THR A 16 LYS A 18 0 SHEET 2 A 6 THR A 26 ASN A 37 -1 O THR A 26 N LYS A 18 SHEET 3 A 6 GLU A 195 TYR A 209 -1 O PHE A 199 N PHE A 36 SHEET 4 A 6 LYS A 158 ASP A 169 1 N LEU A 159 O GLY A 197 SHEET 5 A 6 HIS A 147 ALA A 155 -1 N PHE A 149 O TYR A 164 SHEET 6 A 6 ILE A 129 SER A 131 -1 N VAL A 130 O PHE A 150 SHEET 1 B 2 TRP A 101 THR A 103 0 SHEET 2 B 2 ARG A 107 ILE A 109 -1 O ARG A 107 N THR A 103 SHEET 1 C 2 LYS A 229 ILE A 232 0 SHEET 2 C 2 PHE A 247 GLU A 250 -1 O GLU A 248 N ILE A 231 SHEET 1 D 6 THR B 16 LYS B 18 0 SHEET 2 D 6 THR B 26 ASN B 37 -1 O THR B 26 N LYS B 18 SHEET 3 D 6 GLU B 195 TYR B 209 -1 O PHE B 199 N PHE B 36 SHEET 4 D 6 LYS B 158 ASP B 169 1 N GLN B 165 O THR B 202 SHEET 5 D 6 HIS B 147 ALA B 155 -1 N PHE B 149 O TYR B 164 SHEET 6 D 6 ILE B 129 SER B 131 -1 N VAL B 130 O PHE B 150 SHEET 1 E 2 TRP B 101 PRO B 102 0 SHEET 2 E 2 HIS B 108 ILE B 109 -1 O ILE B 109 N TRP B 101 SHEET 1 F 2 LYS B 229 ILE B 232 0 SHEET 2 F 2 PHE B 247 GLU B 250 -1 O GLU B 248 N ILE B 231 LINK C CXM A 1 N LYS A 2 1555 1555 1.31 LINK C CXM B 1 N LYS B 2 1555 1555 1.30 LINK SG CYS A 146 C6 UMC A 901 1555 1555 2.00 LINK SG CYS B 146 C6 UMC B 301 1555 1555 1.95 LINK O ASN A 76 NA NA A 903 1555 1555 2.41 LINK NA NA A 903 O AHOH A1464 1555 1555 2.53 LINK NA NA A 903 O HOH A1298 1555 1555 2.54 LINK NA NA A 903 O HOH A1465 1555 1555 2.54 LINK NA NA A 903 O HOH A1317 1555 1555 2.59 LINK NA NA A 903 O HOH A1054 1555 1555 2.69 SITE 1 AC1 16 ARG A 21 CYS A 146 HIS A 147 GLN A 165 SITE 2 AC1 16 ARG A 166 SER A 167 CYS A 168 ASP A 169 SITE 3 AC1 16 ASN A 177 HIS A 207 TYR A 209 CB3 A 902 SITE 4 AC1 16 HOH A1020 HOH A1059 ARG B 126 ARG B 127 SITE 1 AC2 26 GLU A 58 ILE A 79 TRP A 80 TRP A 83 SITE 2 AC2 26 LEU A 143 ASP A 169 GLY A 173 PHE A 176 SITE 3 AC2 26 ASN A 177 TYR A 209 VAL A 262 ALA A 263 SITE 4 AC2 26 UMC A 901 HOH A1014 HOH A1031 HOH A1054 SITE 5 AC2 26 HOH A1061 HOH A1064 HOH A1077 HOH A1117 SITE 6 AC2 26 HOH A1130 HOH A1140 HOH A1263 HOH A1317 SITE 7 AC2 26 HOH A1383 HOH A1412 SITE 1 AC3 9 HIS A 51 ARG A 53 ASN A 76 HOH A1054 SITE 2 AC3 9 HOH A1298 HOH A1317 HOH A1345 HOH A1464 SITE 3 AC3 9 HOH A1465 SITE 1 AC4 16 ARG A 126 ARG A 127 ARG B 21 CYS B 146 SITE 2 AC4 16 HIS B 147 GLN B 165 ARG B 166 SER B 167 SITE 3 AC4 16 CYS B 168 ASP B 169 ASN B 177 HIS B 207 SITE 4 AC4 16 TYR B 209 CB3 B 302 HOH B 411 HOH B 415 SITE 1 AC5 26 GLU B 58 ILE B 79 TRP B 80 TRP B 83 SITE 2 AC5 26 LEU B 143 ASP B 169 GLY B 173 PHE B 176 SITE 3 AC5 26 ASN B 177 TYR B 209 ILE B 258 VAL B 262 SITE 4 AC5 26 ALA B 263 UMC B 301 HOH B 422 HOH B 431 SITE 5 AC5 26 HOH B 458 HOH B 460 HOH B 462 HOH B 464 SITE 6 AC5 26 HOH B 480 HOH B 501 HOH B 546 HOH B 594 SITE 7 AC5 26 HOH B 713 HOH B 766 CRYST1 125.410 125.410 66.580 90.00 90.00 120.00 P 63 12 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 0.007974 0.004604 0.000000 0.00000 SCALE2 0.000000 0.009207 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015020 0.00000 HETATM 1 N CXM A 1 103.744 19.973 8.620 1.00 12.43 N ANISOU 1 N CXM A 1 1529 1498 1697 -148 -69 -223 N HETATM 2 CA CXM A 1 102.379 20.404 8.346 1.00 11.97 C ANISOU 2 CA CXM A 1 1424 1463 1663 -296 44 -222 C HETATM 3 CB CXM A 1 101.447 20.070 9.525 1.00 12.81 C ANISOU 3 CB CXM A 1 1331 1536 2000 -243 224 170 C HETATM 4 CG CXM A 1 101.185 18.622 9.715 1.00 14.86 C ANISOU 4 CG CXM A 1 1651 1738 2258 -200 379 -45 C HETATM 5 SD CXM A 1 100.088 18.289 11.106 1.00 14.00 S ANISOU 5 SD CXM A 1 1792 1652 1876 -318 204 -108 S HETATM 6 CE CXM A 1 101.153 18.596 12.482 1.00 16.53 C ANISOU 6 CE CXM A 1 1563 1861 2856 -220 261 354 C HETATM 7 C CXM A 1 102.432 21.924 8.209 1.00 13.16 C ANISOU 7 C CXM A 1 1596 1701 1704 -89 -159 18 C HETATM 8 O CXM A 1 103.235 22.584 8.866 1.00 12.39 O ANISOU 8 O CXM A 1 1580 1505 1623 -211 -34 18 O HETATM 9 CN CXM A 1 104.266 18.812 8.235 1.00 12.76 C ANISOU 9 CN CXM A 1 1423 1609 1816 -403 192 -6 C HETATM 10 ON1 CXM A 1 103.573 17.974 7.611 1.00 12.41 O ANISOU 10 ON1 CXM A 1 1558 1471 1686 -217 227 -104 O HETATM 11 ON2 CXM A 1 105.456 18.563 8.552 1.00 12.23 O ANISOU 11 ON2 CXM A 1 1579 1526 1541 -137 139 -122 O HETATM 12 H CXM A 1 104.014 20.150 9.418 1.00 14.92 H HETATM 13 HA CXM A 1 102.040 19.991 7.525 1.00 14.37 H HETATM 14 HB2 CXM A 1 100.595 20.513 9.389 1.00 15.37 H HETATM 15 HG2 CXM A 1 102.026 18.168 9.881 1.00 17.83 H HETATM 16 HE1 CXM A 1 101.456 19.505 12.444 1.00 19.83 H HETATM 17 HE2 CXM A 1 101.902 17.997 12.436 1.00 19.83 H HETATM 18 HE3 CXM A 1 100.664 18.446 13.294 1.00 19.83 H