HEADER TRANSFERASE 15-JAN-19 6NNR TITLE HIGH-RESOLUTION STRUCTURE OF WILD-TYPE E. COLI THYMIDYLATE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TSASE; COMPND 5 EC: 2.1.1.45; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: THYA, B2827, JW2795; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEOTIDE SYNTHESIS, HYDRIDE TRANSFER, METHYL TRANSFER, CANCER DRUG KEYWDS 2 TARGET, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.M.STROUD,J.FINER-MOORE REVDAT 3 11-OCT-23 6NNR 1 REMARK REVDAT 2 18-DEC-19 6NNR 1 REMARK REVDAT 1 30-JAN-19 6NNR 0 SPRSDE 30-JAN-19 6NNR 4KNZ 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 MG2+ 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 ESSN 1520-5126 JRNL PMID 23611499 JRNL DOI 10.1021/JA400761X REMARK 1 REMARK 1 REFERENCE 1 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 ESSN 1520-5126 REMARK 1 PMID 23034004 REMARK 1 DOI 10.1021/JA307859M REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 277201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.132 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 0.720 REMARK 3 FREE R VALUE TEST SET COUNT : 2007 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 62.8774 - 2.5306 1.00 20044 147 0.1210 0.1313 REMARK 3 2 2.5306 - 2.0086 1.00 19796 145 0.1122 0.1156 REMARK 3 3 2.0086 - 1.7546 1.00 19741 145 0.1021 0.1090 REMARK 3 4 1.7546 - 1.5942 1.00 19731 148 0.0937 0.1136 REMARK 3 5 1.5942 - 1.4799 1.00 19682 140 0.0890 0.1113 REMARK 3 6 1.4799 - 1.3927 1.00 19696 144 0.0967 0.1397 REMARK 3 7 1.3927 - 1.3229 1.00 19720 146 0.1016 0.1257 REMARK 3 8 1.3229 - 1.2653 1.00 19684 139 0.1090 0.1114 REMARK 3 9 1.2653 - 1.2166 1.00 19605 145 0.1190 0.1417 REMARK 3 10 1.2166 - 1.1746 1.00 19637 142 0.1354 0.1405 REMARK 3 11 1.1746 - 1.1379 1.00 19663 146 0.1663 0.1824 REMARK 3 12 1.1379 - 1.1054 1.00 19663 142 0.2075 0.2079 REMARK 3 13 1.1054 - 1.0763 1.00 19547 141 0.2689 0.2711 REMARK 3 14 1.0763 - 1.0500 0.97 18985 137 0.3287 0.3032 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.010 4892 REMARK 3 ANGLE : 1.168 6681 REMARK 3 CHIRALITY : 0.083 689 REMARK 3 PLANARITY : 0.010 874 REMARK 3 DIHEDRAL : 20.251 1836 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 6NNR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-16 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) : 0.8855 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 277308 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 62.765 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 17.84 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.15 REMARK 200 R MERGE FOR SHELL (I) : 2.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.660 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 4KNZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5.2 MG/ML PROTEIN, 17 MM KPO4, 3.3 MM REMARK 280 DUMP, 3.3 MM CB3717, 3.3 MM DTT, AGAINST 1.44 M NA CITRATE, PH REMARK 280 7.4, VAPOR DIFFUSION, 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 33.37850 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 33.37850 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 33.37850 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: 7030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 GLU A 237 CD OE1 OE2 REMARK 470 GLU B 237 CD OE1 OE2 REMARK 470 GLU B 248 CD OE1 OE2 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 HH11 ARG A 49 O HOH A 1003 1.52 REMARK 500 OE1 GLN A 190 HH TYR A 242 1.58 REMARK 500 O HOH A 1063 O HOH A 1350 1.94 REMARK 500 O HOH A 1361 O HOH A 1375 1.97 REMARK 500 NH1 ARG A 49 O HOH A 1003 2.14 REMARK 500 O HOH B 638 O HOH B 652 2.17 REMARK 500 O HOH B 632 O HOH B 636 2.19 REMARK 500 O HOH A 1070 O HOH A 1294 2.19 REMARK 500 O HOH B 647 O HOH B 705 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 1215 O HOH B 458 5555 1.93 REMARK 500 O HOH A 1360 O HOH A 1410 6555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 250 CD GLU A 250 OE1 -0.075 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 VAL A 93 -159.82 -82.59 REMARK 500 ALA A 100 56.30 -160.50 REMARK 500 ASP A 122 65.49 -155.52 REMARK 500 VAL B 93 -159.65 -82.98 REMARK 500 ALA B 100 53.98 -155.60 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 A1173 O 104.0 REMARK 620 3 HOH A1214 O 166.2 89.6 REMARK 620 4 HOH A1275 O 86.7 87.3 91.9 REMARK 620 5 HOH A1342 O 103.0 152.7 63.3 90.2 REMARK 620 6 HOH A1420 O 121.6 109.4 49.7 49.8 51.2 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 EPE A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 905 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CB3 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide UMC B 301 and CYS B REMARK 800 146 DBREF 6NNR A 1 264 UNP P0A884 TYSY_ECOLI 1 264 DBREF 6NNR 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 6NNR CXM A 1 MET MODIFIED RESIDUE MODRES 6NNR CXM B 1 MET MODIFIED RESIDUE HET CXM A 1 17 HET CXM B 1 17 HET UMC A 901 27 HET CB3 A 902 56 HET NA A 903 1 HET EPE A 904 15 HET EPE A 905 32 HET UMC B 301 27 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 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES 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 6 EPE 2(C8 H18 N2 O4 S) FORMUL 10 HOH *753(H2 O) HELIX 1 AA1 CXM A 1 GLY A 15 1 15 HELIX 2 AA2 GLN A 39 GLY A 41 5 3 HELIX 3 AA3 HIS A 51 GLY A 65 1 15 HELIX 4 AA4 ILE A 69 ASN A 75 1 7 HELIX 5 AA5 TRP A 80 ALA A 84 5 5 HELIX 6 AA6 VAL A 93 ALA A 100 1 8 HELIX 7 AA7 ASP A 110 ASP A 122 1 13 HELIX 8 AA8 ASN A 134 MET A 141 5 8 HELIX 9 AA9 LEU A 172 ASP A 193 1 22 HELIX 10 AB1 HIS A 212 SER A 221 1 10 HELIX 11 AB2 ARG A 243 GLU A 245 5 3 HELIX 12 AB3 LYS B 2 GLY B 15 1 14 HELIX 13 AB4 GLN B 39 GLY B 41 5 3 HELIX 14 AB5 HIS B 51 GLN B 64 1 14 HELIX 15 AB6 ILE B 69 ASN B 75 1 7 HELIX 16 AB7 TRP B 80 ALA B 84 5 5 HELIX 17 AB8 VAL B 93 ALA B 100 1 8 HELIX 18 AB9 ASP B 110 ASP B 122 1 13 HELIX 19 AC1 ASN B 134 MET B 141 5 8 HELIX 20 AC2 LEU B 172 ASP B 193 1 22 HELIX 21 AC3 HIS B 212 SER B 221 1 10 HELIX 22 AC4 ARG B 243 GLU B 245 5 3 SHEET 1 AA1 6 THR A 16 LYS A 18 0 SHEET 2 AA1 6 THR A 26 ASN A 37 -1 O THR A 26 N LYS A 18 SHEET 3 AA1 6 GLU A 195 TYR A 209 -1 O TRP A 201 N MET A 34 SHEET 4 AA1 6 LYS A 158 ASP A 169 1 N GLN A 165 O THR A 202 SHEET 5 AA1 6 HIS A 147 ALA A 155 -1 N PHE A 149 O TYR A 164 SHEET 6 AA1 6 ILE A 129 SER A 131 -1 N VAL A 130 O PHE A 150 SHEET 1 AA2 2 TRP A 101 PRO A 102 0 SHEET 2 AA2 2 HIS A 108 ILE A 109 -1 O ILE A 109 N TRP A 101 SHEET 1 AA3 2 LYS A 229 ILE A 232 0 SHEET 2 AA3 2 PHE A 247 GLU A 250 -1 O GLU A 250 N LYS A 229 SHEET 1 AA4 6 THR B 16 LYS B 18 0 SHEET 2 AA4 6 THR B 26 ASN B 37 -1 O SER B 28 N THR B 16 SHEET 3 AA4 6 GLU B 195 TYR B 209 -1 O PHE B 199 N PHE B 36 SHEET 4 AA4 6 LYS B 158 ASP B 169 1 N GLN B 165 O THR B 202 SHEET 5 AA4 6 HIS B 147 ALA B 155 -1 N PHE B 149 O TYR B 164 SHEET 6 AA4 6 ILE B 129 SER B 131 -1 N VAL B 130 O PHE B 150 SHEET 1 AA5 2 TRP B 101 PRO B 102 0 SHEET 2 AA5 2 HIS B 108 ILE B 109 -1 O ILE B 109 N TRP B 101 SHEET 1 AA6 2 LYS B 229 ILE B 232 0 SHEET 2 AA6 2 PHE B 247 GLU B 250 -1 O GLU B 250 N LYS B 229 LINK C CXM A 1 N LYS A 2 1555 1555 1.33 LINK SG CYS A 146 C6 UMC A 901 1555 1555 1.87 LINK C CXM B 1 N LYS B 2 1555 1555 1.31 LINK SG CYS B 146 C6 UMC B 301 1555 1555 1.87 LINK O ASN A 76 NA NA A 903 1555 1555 2.34 LINK NA NA A 903 O HOH A1173 1555 1555 2.72 LINK NA NA A 903 O HOH A1214 1555 1555 2.51 LINK NA NA A 903 O HOH A1275 1555 1555 2.28 LINK NA NA A 903 O HOH A1342 1555 1555 2.39 LINK NA NA A 903 O HOH A1420 1555 1555 3.12 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 TYR A 209 CB3 A 902 SITE 4 AC1 16 HOH A1117 HOH A1146 ARG B 126 ARG B 127 SITE 1 AC2 26 HIS A 51 GLU A 58 ILE A 79 TRP A 80 SITE 2 AC2 26 TRP A 83 LEU A 143 ASP A 169 GLY A 173 SITE 3 AC2 26 PHE A 176 ASN A 177 TYR A 209 VAL A 262 SITE 4 AC2 26 ALA A 263 UMC A 901 HOH A1073 HOH A1079 SITE 5 AC2 26 HOH A1086 HOH A1121 HOH A1129 HOH A1134 SITE 6 AC2 26 HOH A1142 HOH A1171 HOH A1173 HOH A1214 SITE 7 AC2 26 HOH A1239 HOH A1250 SITE 1 AC3 6 HIS A 51 ASN A 76 HOH A1173 HOH A1214 SITE 2 AC3 6 HOH A1275 HOH A1342 SITE 1 AC4 12 GLN A 39 GLU A 195 HOH A1033 HOH A1046 SITE 2 AC4 12 HOH A1056 HOH A1062 HOH A1064 HOH A1130 SITE 3 AC4 12 HOH A1258 LYS B 120 ASP B 193 LYS B 235 SITE 1 AC5 8 ALA A 155 ASP A 156 GLY A 157 HOH A1007 SITE 2 AC5 8 HOH A1031 HOH A1138 HIS B 217 SER B 221 SITE 1 AC6 25 GLU B 58 ILE B 79 TRP B 80 TRP B 83 SITE 2 AC6 25 LEU B 143 ASP B 169 GLY B 173 PHE B 176 SITE 3 AC6 25 ASN B 177 TYR B 209 ILE B 258 VAL B 262 SITE 4 AC6 25 ALA B 263 UMC B 301 HOH B 440 HOH B 443 SITE 5 AC6 25 HOH B 445 HOH B 482 HOH B 487 HOH B 516 SITE 6 AC6 25 HOH B 535 HOH B 536 HOH B 572 HOH B 626 SITE 7 AC6 25 HOH B 639 SITE 1 AC7 19 ARG A 126 ARG A 127 ARG B 21 TYR B 94 SITE 2 AC7 19 ALA B 144 PRO B 145 HIS B 147 ALA B 148 SITE 3 AC7 19 GLN B 165 ARG B 166 SER B 167 CYS B 168 SITE 4 AC7 19 ASP B 169 ASN B 177 HIS B 207 TYR B 209 SITE 5 AC7 19 CB3 B 302 HOH B 464 HOH B 493 CRYST1 125.530 125.530 66.757 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 0.007966 0.004599 0.000000 0.00000 SCALE2 0.000000 0.009199 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014980 0.00000 HETATM 1 N CXM A 1 -6.441 28.676 31.484 1.00 8.85 N ANISOU 1 N CXM A 1 1081 1166 1114 -72 -201 84 N HETATM 2 CA CXM A 1 -6.149 30.079 31.774 1.00 9.14 C ANISOU 2 CA CXM A 1 1084 1307 1082 -162 -56 74 C HETATM 3 CB CXM A 1 -5.393 30.759 30.621 1.00 10.27 C ANISOU 3 CB CXM A 1 1144 1239 1521 -107 137 52 C HETATM 4 CG CXM A 1 -4.009 30.236 30.379 1.00 10.94 C ANISOU 4 CG CXM A 1 1278 1504 1376 -30 42 154 C HETATM 5 SD CXM A 1 -3.159 31.019 29.006 1.00 10.99 S ANISOU 5 SD CXM A 1 1261 1707 1206 -138 -40 292 S HETATM 6 CE CXM A 1 -3.947 30.223 27.612 1.00 12.48 C ANISOU 6 CE CXM A 1 1415 1379 1946 -341 399 -31 C HETATM 7 C CXM A 1 -7.482 30.784 31.941 1.00 8.88 C ANISOU 7 C CXM A 1 1256 1333 784 -174 -51 -28 C HETATM 8 O CXM A 1 -8.462 30.448 31.271 1.00 9.06 O ANISOU 8 O CXM A 1 1158 1264 1021 -62 -137 30 O HETATM 9 CN CXM A 1 -5.695 27.638 31.889 1.00 8.73 C ANISOU 9 CN CXM A 1 1185 1239 893 -109 -34 38 C HETATM 10 ON1 CXM A 1 -6.096 26.484 31.579 1.00 9.28 O ANISOU 10 ON1 CXM A 1 1128 1338 1061 -10 -64 61 O HETATM 11 ON2 CXM A 1 -4.618 27.822 32.521 1.00 9.34 O ANISOU 11 ON2 CXM A 1 1191 1373 984 -70 -142 144 O HETATM 12 HA CXM A 1 -5.620 30.154 32.596 1.00 10.97 H HETATM 13 HB2 CXM A 1 -5.327 31.709 30.805 1.00 12.33 H HETATM 14 HG2 CXM A 1 -4.059 29.284 30.198 1.00 13.13 H HETATM 15 HE1 CXM A 1 -4.888 30.408 27.637 1.00 14.97 H HETATM 16 HE2 CXM A 1 -3.797 29.276 27.667 1.00 14.97 H HETATM 17 HE3 CXM A 1 -3.567 30.568 26.800 1.00 14.97 H