HEADER TRANSFERASE 26-OCT-20 7DCM TITLE CRYSTAL STRUCTURE OF CITX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE APO-CITRATE LYASE PHOSPHORIBOSYL-DEPHOSPHO-COA COMPND 3 TRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: APO-CITRATE LYASE PHOSPHORIBOSYL-DEPHOSPHO-COA TRANSFERASE, COMPND 6 APO-ACP NUCLEODITYLTRANSFERASE,HOLO-ACP SYNTHASE,HOLO-CITRATE LYASE COMPND 7 SYNTHASE; COMPND 8 EC: 2.7.7.61; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS ZINC FINGER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.XU,B.WANG,X.D.SU REVDAT 2 17-MAY-23 7DCM 1 JRNL REVDAT 1 03-NOV-21 7DCM 0 JRNL AUTH Y.CHENG,H.WANG,H.XU,Y.LIU,B.MA,X.CHEN,X.ZENG,X.WANG,B.WANG, JRNL AUTH 2 C.SHIAU,S.OVCHINNIKOV,X.D.SU,C.WANG JRNL TITL CO-EVOLUTION-BASED PREDICTION OF METAL-BINDING SITES IN JRNL TITL 2 PROTEOMES BY MACHINE LEARNING. JRNL REF NAT.CHEM.BIOL. V. 19 548 2023 JRNL REFN ESSN 1552-4469 JRNL PMID 36593274 JRNL DOI 10.1038/S41589-022-01223-Z REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 5374 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 540 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 10.0000 - 4.7619 0.98 1286 155 0.1704 0.2188 REMARK 3 2 4.7619 - 3.7842 1.00 1314 143 0.1429 0.2026 REMARK 3 3 3.7842 - 3.3072 1.00 1327 149 0.1644 0.2633 REMARK 3 4 3.3072 - 3.0054 1.00 1321 148 0.1850 0.2715 REMARK 3 5 3.0054 - 2.7903 1.00 1339 134 0.1964 0.2773 REMARK 3 6 2.7903 - 2.6260 1.00 1297 141 0.1955 0.3969 REMARK 3 7 2.6260 - 2.4960 0.97 1321 146 0.1894 0.3565 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.62 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 : 0.009 1444 REMARK 3 ANGLE : 1.074 1964 REMARK 3 CHIRALITY : 0.055 227 REMARK 3 PLANARITY : 0.007 256 REMARK 3 DIHEDRAL : 6.767 888 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 7DCM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019156. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5375 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.495 REMARK 200 RESOLUTION RANGE LOW (A) : 24.439 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 40.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 18.39200 REMARK 290 SMTRY3 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 CYS A 180 REMARK 465 ASN A 181 REMARK 465 VAL A 182 REMARK 465 ASN A 183 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 ASP A 53 76.01 -112.91 REMARK 500 ARG A 157 -78.09 -51.19 REMARK 500 LYS A 159 74.83 -62.17 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 145 SG REMARK 620 2 CYS A 148 SG 132.4 REMARK 620 3 CYS A 155 SG 98.6 108.0 REMARK 620 4 HIS A 161 NE2 96.1 111.7 107.7 REMARK 620 N 1 2 3 DBREF 7DCM A 1 183 UNP C3TJT2 C3TJT2_ECOLX 1 183 SEQADV 7DCM GLY A -2 UNP C3TJT2 EXPRESSION TAG SEQADV 7DCM SER A -1 UNP C3TJT2 EXPRESSION TAG SEQADV 7DCM HIS A 0 UNP C3TJT2 EXPRESSION TAG SEQRES 1 A 186 GLY SER HIS MSE HIS LEU LEU PRO GLU LEU ALA SER HIS SEQRES 2 A 186 HIS ALA VAL SER ILE PRO GLU LEU LEU VAL SER ARG ASP SEQRES 3 A 186 GLU ARG GLN ALA ARG GLN HIS VAL TRP LEU LYS ARG HIS SEQRES 4 A 186 PRO VAL PRO LEU VAL SER PHE THR VAL VAL ALA PRO GLY SEQRES 5 A 186 PRO ILE LYS ASP SER GLU VAL THR ARG ARG ILE PHE ASN SEQRES 6 A 186 HIS GLY VAL THR ALA LEU ARG ALA LEU ALA ALA LYS GLN SEQRES 7 A 186 GLY TRP GLN ILE GLN GLU GLN ALA ALA LEU VAL SER ALA SEQRES 8 A 186 SER GLY PRO GLU GLY MSE LEU SER ILE ALA ALA PRO ALA SEQRES 9 A 186 ARG ASP LEU LYS LEU ALA THR ILE GLU LEU GLU HIS SER SEQRES 10 A 186 HIS PRO LEU GLY ARG LEU TRP ASP ILE ASP VAL LEU THR SEQRES 11 A 186 PRO GLU GLY GLU ILE LEU SER ARG ARG ASP TYR SER LEU SEQRES 12 A 186 PRO PRO ARG ARG CYS LEU LEU CYS GLU GLN SER ALA ALA SEQRES 13 A 186 VAL CYS ALA ARG GLY LYS THR HIS GLN LEU THR ASP LEU SEQRES 14 A 186 LEU ASN ARG MSE GLU ALA LEU LEU ASN ASP VAL ASP ALA SEQRES 15 A 186 CYS ASN VAL ASN MODRES 7DCM MSE A 1 MET MODIFIED RESIDUE MODRES 7DCM MSE A 94 MET MODIFIED RESIDUE MODRES 7DCM MSE A 170 MET MODIFIED RESIDUE HET MSE A 1 8 HET MSE A 94 8 HET MSE A 170 8 HET ZN A 201 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *35(H2 O) HELIX 1 AA1 LEU A 4 ALA A 8 5 5 HELIX 2 AA2 SER A 14 HIS A 36 1 23 HELIX 3 AA3 SER A 54 GLN A 75 1 22 HELIX 4 AA4 PRO A 100 HIS A 115 1 16 HELIX 5 AA5 LEU A 117 ARG A 119 5 3 HELIX 6 AA6 SER A 134 SER A 139 5 6 HELIX 7 AA7 SER A 151 GLY A 158 1 8 HELIX 8 AA8 GLN A 162 ASP A 178 1 17 SHEET 1 AA1 4 GLN A 78 SER A 87 0 SHEET 2 AA1 4 GLY A 90 ALA A 98 -1 O SER A 96 N GLU A 81 SHEET 3 AA1 4 LEU A 40 VAL A 45 -1 N PHE A 43 O GLY A 93 SHEET 4 AA1 4 TRP A 121 LEU A 126 -1 O ASP A 122 N THR A 44 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N HIS A 2 1555 1555 1.32 LINK C GLY A 93 N MSE A 94 1555 1555 1.33 LINK C MSE A 94 N LEU A 95 1555 1555 1.33 LINK C ARG A 169 N MSE A 170 1555 1555 1.33 LINK C MSE A 170 N GLU A 171 1555 1555 1.34 LINK SG CYS A 145 ZN ZN A 201 1555 1555 2.41 LINK SG CYS A 148 ZN ZN A 201 1555 1555 2.44 LINK SG CYS A 155 ZN ZN A 201 1555 1555 2.28 LINK NE2 HIS A 161 ZN ZN A 201 1555 1555 2.02 CRYST1 43.017 36.784 48.265 90.00 92.13 90.00 P 1 21 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 0.023247 0.000000 0.000863 0.00000 SCALE2 0.000000 0.027186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020733 0.00000