HEADER TRANSFERASE 02-AUG-12 4GEV TITLE E. COLI THYMIDYLATE SYNTHASE Y209W VARIANT IN COMPLEX WITH SUBSTRATE TITLE 2 AND A COFACTOR ANALOG 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; COMPND 7 MUTATION: 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 BETA SHEET, ALPHA/BETA PROTEIN, METHYLASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.NEWBY,T.T.LEE,J.FINER-MOORE,R.M.STROUD REVDAT 4 15-NOV-17 4GEV 1 REMARK REVDAT 3 07-NOV-12 4GEV 1 JRNL REVDAT 2 17-OCT-12 4GEV 1 JRNL REVDAT 1 29-AUG-12 4GEV 0 SPRSDE 29-AUG-12 4GEV 2G8M JRNL AUTH Z.WANG,T.ABEYSINGHE,J.S.FINER-MOORE,R.M.STROUD,A.KOHEN JRNL TITL A REMOTE MUTATION AFFECTS THE HYDRIDE TRANSFER BY DISRUPTING JRNL TITL 2 CONCERTED PROTEIN MOTIONS IN THYMIDYLATE SYNTHASE. JRNL REF J.AM.CHEM.SOC. V. 134 17722 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 23034004 JRNL DOI 10.1021/JA307859M 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 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 45.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 146990 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.128 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 7362 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 45.8623 - 4.0443 0.99 4760 232 0.1519 0.1610 REMARK 3 2 4.0443 - 3.2103 1.00 4708 230 0.1210 0.1357 REMARK 3 3 3.2103 - 2.8046 1.00 4683 236 0.1405 0.1466 REMARK 3 4 2.8046 - 2.5482 1.00 4696 245 0.1283 0.1585 REMARK 3 5 2.5482 - 2.3655 1.00 4659 249 0.1179 0.1441 REMARK 3 6 2.3655 - 2.2261 1.00 4664 252 0.1042 0.1247 REMARK 3 7 2.2261 - 2.1146 1.00 4684 238 0.1028 0.1313 REMARK 3 8 2.1146 - 2.0225 1.00 4677 232 0.1064 0.1273 REMARK 3 9 2.0225 - 1.9447 1.00 4684 234 0.1015 0.1349 REMARK 3 10 1.9447 - 1.8776 1.00 4624 246 0.1011 0.1251 REMARK 3 11 1.8776 - 1.8189 1.00 4701 222 0.0934 0.1237 REMARK 3 12 1.8189 - 1.7669 1.00 4644 252 0.0891 0.1255 REMARK 3 13 1.7669 - 1.7203 1.00 4646 265 0.0936 0.1336 REMARK 3 14 1.7203 - 1.6784 1.00 4636 261 0.0964 0.1323 REMARK 3 15 1.6784 - 1.6402 1.00 4640 251 0.0960 0.1289 REMARK 3 16 1.6402 - 1.6053 1.00 4683 236 0.1031 0.1502 REMARK 3 17 1.6053 - 1.5732 1.00 4617 260 0.1024 0.1549 REMARK 3 18 1.5732 - 1.5435 1.00 4664 254 0.1094 0.1512 REMARK 3 19 1.5435 - 1.5159 1.00 4608 243 0.1173 0.1487 REMARK 3 20 1.5159 - 1.4902 1.00 4644 264 0.1282 0.1844 REMARK 3 21 1.4902 - 1.4662 1.00 4645 270 0.1380 0.1761 REMARK 3 22 1.4662 - 1.4436 1.00 4612 248 0.1437 0.1797 REMARK 3 23 1.4436 - 1.4224 1.00 4639 234 0.1617 0.2010 REMARK 3 24 1.4224 - 1.4024 1.00 4659 232 0.1781 0.2197 REMARK 3 25 1.4024 - 1.3834 1.00 4657 244 0.1958 0.2335 REMARK 3 26 1.3834 - 1.3655 1.00 4648 247 0.2012 0.2493 REMARK 3 27 1.3655 - 1.3484 1.00 4619 245 0.2190 0.2460 REMARK 3 28 1.3484 - 1.3321 1.00 4617 238 0.2225 0.2332 REMARK 3 29 1.3321 - 1.3166 1.00 4669 254 0.2601 0.2631 REMARK 3 30 1.3166 - 1.3000 0.98 4541 248 0.2753 0.2998 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 : 40.88 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.510 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.24320 REMARK 3 B22 (A**2) : -0.24320 REMARK 3 B33 (A**2) : 0.48640 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 : 0.008 4572 REMARK 3 ANGLE : 1.348 6223 REMARK 3 CHIRALITY : 0.082 645 REMARK 3 PLANARITY : 0.007 805 REMARK 3 DIHEDRAL : 16.316 1683 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 4GEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-02 REMARK 200 TEMPERATURE (KELVIN) : 103 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) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI (111) REMARK 200 OPTICS : MONOCHROMATOR, DOUBLE CRYSTAL SI REMARK 200 (111) 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 : 146991 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 45.834 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.000 REMARK 200 R MERGE (I) : 0.08000 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) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.82300 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: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION AGAINST 1.44 M SODIUM REMARK 280 CITRATE, HEPES FROM 5.2 MG/ML PROTEIN SOLUTION CONTAINING 17MM REMARK 280 KPO4, DTT, 3.3 MM DUMP, 3.3 MM CB3717 AND EITHER 0.5% REMARK 280 ETHYLACETATE OR 4% N-PROPANOL, PH 7.4, VAPOR DIFFUSION, HANGING REMARK 280 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 33.46900 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 33.46900 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 33.46900 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: 6430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 HE2 HIS B 207 HO3' UMC B 801 1.08 REMARK 500 HE2 HIS A 207 HO3' UMC A 701 1.10 REMARK 500 O HOH B 927 O HOH B 1188 2.00 REMARK 500 O HOH A 1021 O HOH A 1131 2.04 REMARK 500 O HOH A 1033 O HOH A 1096 2.06 REMARK 500 O HOH B 1046 O HOH B 1112 2.06 REMARK 500 O HOH A 868 O HOH A 965 2.11 REMARK 500 O SER A 210 O HOH A 1126 2.16 REMARK 500 O HOH A 868 O HOH B 942 2.17 REMARK 500 O HOH A 1096 O HOH A 1172 2.17 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 1089 O HOH A 1141 6544 2.14 REMARK 500 O HOH A 950 O HOH A 1141 6544 2.18 REMARK 500 O HOH A 1089 O HOH B 1096 6544 2.19 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 56.76 -160.96 REMARK 500 ASP A 122 59.79 -150.53 REMARK 500 ARG B 21 -46.49 -29.24 REMARK 500 ALA B 100 58.48 -155.81 REMARK 500 ASP B 122 59.23 -144.80 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 UMC A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CB3 A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMC B 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CB3 B 802 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G8X RELATED DB: PDB REMARK 900 E. COLI Y209W THYMIDYLATE SYNTHASE APO ENZYME REMARK 900 RELATED ID: 2G8O RELATED DB: PDB REMARK 900 WILD TYPE E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP AND REMARK 900 CB3717 REMARK 900 RELATED ID: 2G86 RELATED DB: PDB REMARK 900 L. CASEI THYMIDYLATE SYNTHASE Y261F-DUMP REMARK 900 RELATED ID: 2G89 RELATED DB: PDB REMARK 900 L. CASEI THYMIDYLATE SYNTHASE Y261A-DUMP REMARK 900 RELATED ID: 2G8A RELATED DB: PDB REMARK 900 L. CASEI THYMIDYLATE SYNTHASE Y261M-DUMP REMARK 900 RELATED ID: 2G8D RELATED DB: PDB REMARK 900 L. CASEI THYMIDYLATE SYNTHASE Y261A-DUMP DBREF 4GEV A 1 264 UNP P0A884 TYSY_ECOLI 1 264 DBREF 4GEV B 1 264 UNP P0A884 TYSY_ECOLI 1 264 SEQADV 4GEV TRP A 209 UNP P0A884 TYR 209 ENGINEERED MUTATION SEQADV 4GEV TRP B 209 UNP P0A884 TYR 209 ENGINEERED MUTATION 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 TRP 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 TRP 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 4GEV CXM A 1 MET N-CARBOXYMETHIONINE MODRES 4GEV CXM B 1 MET N-CARBOXYMETHIONINE HET CXM A 1 18 HET CXM B 1 18 HET UMC A 701 32 HET CB3 A 702 56 HET UMC B 801 32 HET CB3 B 802 56 HETNAM CXM N-CARBOXYMETHIONINE HETNAM UMC 2'-DEOXY-5'-URIDYLIC ACID HETNAM CB3 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID 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 7 HOH *673(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 GLY A 173 CYS A 192 1 20 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 GLY B 65 1 15 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 TRP A 209 -1 O PHE A 199 N PHE A 36 SHEET 4 A 6 LYS A 158 ASP A 169 1 N GLN A 165 O THR A 202 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 PRO A 102 0 SHEET 2 B 2 HIS A 108 ILE A 109 -1 O ILE A 109 N TRP A 101 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 250 N LYS A 229 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 TRP 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 TYR B 153 O SER B 160 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 1.33 LINK C CXM B 1 N LYS B 2 1555 1555 1.33 LINK SG CYS A 146 C6 UMC A 701 1555 1555 2.06 LINK SG CYS B 146 C6 UMC B 801 1555 1555 2.12 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 TRP A 209 CB3 A 702 SITE 4 AC1 16 HOH A 820 HOH A 859 ARG B 126 ARG B 127 SITE 1 AC2 23 GLU A 58 ILE A 79 TRP A 80 TRP A 83 SITE 2 AC2 23 LEU A 143 ASP A 169 GLY A 173 PHE A 176 SITE 3 AC2 23 ASN A 177 VAL A 262 ALA A 263 UMC A 701 SITE 4 AC2 23 HOH A 814 HOH A 831 HOH A 854 HOH A 861 SITE 5 AC2 23 HOH A 864 HOH A 880 HOH A 925 HOH A 941 SITE 6 AC2 23 HOH A 957 HOH A1145 HOH A1183 SITE 1 AC3 16 ARG A 126 ARG A 127 ARG B 21 CYS B 146 SITE 2 AC3 16 HIS B 147 GLN B 165 ARG B 166 SER B 167 SITE 3 AC3 16 CYS B 168 ASP B 169 ASN B 177 HIS B 207 SITE 4 AC3 16 TRP B 209 CB3 B 802 HOH B 911 HOH B 915 SITE 1 AC4 20 GLU B 58 ILE B 79 TRP B 80 TRP B 83 SITE 2 AC4 20 ASP B 169 GLY B 173 PHE B 176 ASN B 177 SITE 3 AC4 20 VAL B 262 ALA B 263 UMC B 801 HOH B 922 SITE 4 AC4 20 HOH B 931 HOH B 961 HOH B 963 HOH B 967 SITE 5 AC4 20 HOH B 969 HOH B 992 HOH B1025 HOH B1110 CRYST1 125.778 125.778 66.938 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 0.007951 0.004590 0.000000 0.00000 SCALE2 0.000000 0.009180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014939 0.00000 HETATM 1 N CXM A 1 103.990 20.180 8.587 1.00 10.52 N ANISOU 1 N CXM A 1 1308 1600 1087 -369 -91 -133 N HETATM 2 CA CXM A 1 102.637 20.632 8.295 1.00 10.79 C ANISOU 2 CA CXM A 1 1364 1596 1139 -478 -84 -18 C HETATM 3 CB CXM A 1 101.696 20.293 9.456 1.00 12.88 C ANISOU 3 CB CXM A 1 1415 1926 1553 -434 115 299 C HETATM 4 CG CXM A 1 101.466 18.829 9.657 1.00 14.16 C ANISOU 4 CG CXM A 1 1704 2074 1600 -303 478 -57 C HETATM 5 SD CXM A 1 100.387 18.508 11.060 1.00 14.07 S ANISOU 5 SD CXM A 1 2010 1992 1344 -486 409 -178 S HETATM 6 CE CXM A 1 101.418 18.801 12.424 1.00 15.83 C ANISOU 6 CE CXM A 1 1593 2346 2074 -581 128 364 C HETATM 7 C CXM A 1 102.682 22.142 8.159 1.00 10.70 C ANISOU 7 C CXM A 1 1535 1708 822 -208 -196 61 C HETATM 8 O CXM A 1 103.480 22.799 8.821 1.00 10.86 O ANISOU 8 O CXM A 1 1484 1605 1036 -243 -304 -34 O HETATM 9 CN CXM A 1 104.505 19.037 8.144 1.00 10.55 C ANISOU 9 CN CXM A 1 1421 1655 933 -446 -173 -269 C HETATM 10 ON1 CXM A 1 105.701 18.782 8.430 1.00 11.03 O ANISOU 10 ON1 CXM A 1 1500 1816 876 -218 -29 -119 O HETATM 11 ON2 CXM A 1 103.803 18.203 7.525 1.00 11.05 O ANISOU 11 ON2 CXM A 1 1534 1548 1114 -338 71 -228 O HETATM 12 H CXM A 1 104.585 20.798 8.526 1.00 12.61 H HETATM 13 HA CXM A 1 102.305 20.220 7.470 1.00 12.93 H HETATM 14 HB2 CXM A 1 100.836 20.712 9.299 1.00 15.44 H HETATM 15 HG2 CXM A 1 102.317 18.396 9.828 1.00 16.97 H HETATM 16 HE1 CXM A 1 101.726 19.710 12.392 1.00 18.98 H HETATM 17 HE2 CXM A 1 102.166 18.200 12.385 1.00 18.98 H HETATM 18 HE3 CXM A 1 100.919 18.652 13.230 1.00 18.98 H