HEADER TRANSFERASE/DNA 22-AUG-13 4MDF TITLE STRUCTURE OF BACTERIAL POLYNUCLEOTIDE KINASE MICHAELIS COMPLEX BOUND TITLE 2 TO GTP AND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: METALLOPHOSPHOESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*CP*CP*TP*GP*T)-3'); COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM THERMOCELLUM; SOURCE 3 ORGANISM_TAXID: 203119; SOURCE 4 STRAIN: ATCC 27405 / DSM 1237; SOURCE 5 GENE: CTHE_2768; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: OBTAINED FROM COMMERCIAL SYNTHETIC SOURCE KEYWDS RNA REPAIR, P-LOOP PHOSPHOTRANSFERASE, TRANSFERASE, HYDROLASE-DNA KEYWDS 2 COMPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.SHUMAN,U.DAS,L.K.WANG,P.SMITH,A.JACEWICZ REVDAT 3 28-FEB-24 4MDF 1 REMARK SEQADV LINK REVDAT 2 12-FEB-14 4MDF 1 JRNL REVDAT 1 06-NOV-13 4MDF 0 JRNL AUTH U.DAS,L.K.WANG,P.SMITH,A.JACEWICZ,S.SHUMAN JRNL TITL STRUCTURES OF BACTERIAL POLYNUCLEOTIDE KINASE IN A MICHAELIS JRNL TITL 2 COMPLEX WITH GTP*MG2+ AND 5'-OH OLIGONUCLEOTIDE AND A JRNL TITL 3 PRODUCT COMPLEX WITH GDP*MG2+ AND 5'-PO4 OLIGONUCLEOTIDE JRNL TITL 4 REVEAL A MECHANISM OF GENERAL ACID-BASE CATALYSIS AND THE JRNL TITL 5 DETERMINANTS OF PHOSPHOACCEPTOR RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 42 1152 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24150947 JRNL DOI 10.1093/NAR/GKT936 REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 49036 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.950 REMARK 3 FREE R VALUE TEST SET COUNT : 3896 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 48.4842 - 5.2429 1.00 1776 152 0.1932 0.1998 REMARK 3 2 5.2429 - 4.1622 1.00 1674 145 0.1422 0.1574 REMARK 3 3 4.1622 - 3.6362 1.00 1666 139 0.1445 0.1648 REMARK 3 4 3.6362 - 3.3039 1.00 1634 143 0.1650 0.1915 REMARK 3 5 3.3039 - 3.0671 1.00 1660 136 0.1683 0.2129 REMARK 3 6 3.0671 - 2.8863 1.00 1645 131 0.1707 0.1882 REMARK 3 7 2.8863 - 2.7418 1.00 1609 155 0.1728 0.1965 REMARK 3 8 2.7418 - 2.6224 1.00 1620 136 0.1712 0.2090 REMARK 3 9 2.6224 - 2.5215 1.00 1620 136 0.1816 0.2116 REMARK 3 10 2.5215 - 2.4345 1.00 1593 156 0.1633 0.1964 REMARK 3 11 2.4345 - 2.3583 1.00 1655 122 0.1615 0.2080 REMARK 3 12 2.3583 - 2.2909 1.00 1606 124 0.1570 0.2177 REMARK 3 13 2.2909 - 2.2306 1.00 1611 150 0.1562 0.2170 REMARK 3 14 2.2306 - 2.1762 1.00 1599 141 0.1517 0.1664 REMARK 3 15 2.1762 - 2.1267 1.00 1578 144 0.1587 0.2235 REMARK 3 16 2.1267 - 2.0815 1.00 1587 150 0.1570 0.1999 REMARK 3 17 2.0815 - 2.0398 1.00 1586 136 0.1586 0.1897 REMARK 3 18 2.0398 - 2.0013 0.99 1602 150 0.1569 0.1948 REMARK 3 19 2.0013 - 1.9656 1.00 1585 124 0.1587 0.2129 REMARK 3 20 1.9656 - 1.9323 0.99 1635 143 0.1475 0.1938 REMARK 3 21 1.9323 - 1.9011 0.99 1591 119 0.1518 0.1975 REMARK 3 22 1.9011 - 1.8719 1.00 1598 123 0.1488 0.1802 REMARK 3 23 1.8719 - 1.8443 0.99 1575 136 0.1534 0.2068 REMARK 3 24 1.8443 - 1.8183 0.99 1593 140 0.1643 0.2199 REMARK 3 25 1.8183 - 1.7938 0.99 1577 137 0.1671 0.2187 REMARK 3 26 1.7938 - 1.7705 0.99 1572 133 0.1813 0.1957 REMARK 3 27 1.7705 - 1.7483 0.98 1561 157 0.1941 0.2592 REMARK 3 28 1.7483 - 1.7273 0.97 1532 138 0.2233 0.2766 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.830 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) : 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 : 0.006 3080 REMARK 3 ANGLE : 1.126 4211 REMARK 3 CHIRALITY : 0.070 476 REMARK 3 PLANARITY : 0.005 506 REMARK 3 DIHEDRAL : 20.110 1211 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 4MDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49311 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.727 REMARK 200 RESOLUTION RANGE LOW (A) : 53.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, PH 5.0, 2 MM REMARK 280 GUANOSINE TRIPHOSPHATE, 100MM MAGNESIUM CHLORIDE,18-24% PEG 6000, REMARK 280 1.1 MM SHORT DNA STRAND, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 26.51250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.73000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.37750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.73000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.51250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.37750 REMARK 290 SMTRY3 4 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 DT C 5 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT C 5 C7 C6 REMARK 470 DT D 5 C5' C4' O4' C3' O3' C2' C1' REMARK 470 DT D 5 N1 C2 O2 N3 C4 O4 C5 REMARK 470 DT D 5 C7 C6 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 1273 O HOH B 1277 2.03 REMARK 500 O HOH B 1268 O HOH B 1271 2.14 REMARK 500 O HOH B 1273 O HOH B 1279 2.15 REMARK 500 O HOH A 1181 O HOH B 1229 2.16 REMARK 500 O HOH B 1136 O HOH B 1271 2.17 REMARK 500 O HOH A 1177 O HOH A 1244 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 1259 O HOH B 1272 2455 2.10 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 DT D 3 O4' - C1' - N1 ANGL. DEV. = 2.0 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 ASP A 46 -7.45 75.68 REMARK 500 ASP B 46 -7.33 74.43 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 MG A1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 22 OG REMARK 620 2 GTP A1001 O1B 89.4 REMARK 620 3 GTP A1001 O3G 178.4 90.2 REMARK 620 4 HOH A1101 O 87.3 175.6 93.0 REMARK 620 5 HOH A1102 O 90.1 88.5 88.4 88.6 REMARK 620 6 HOH A1103 O 87.1 94.0 94.4 88.7 176.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 22 OG REMARK 620 2 GTP B1001 O3G 177.6 REMARK 620 3 GTP B1001 O1B 89.5 91.2 REMARK 620 4 HOH B1101 O 86.2 91.5 92.3 REMARK 620 5 HOH B1102 O 86.6 92.6 175.8 85.7 REMARK 620 6 HOH B1103 O 91.2 91.1 90.5 176.1 91.3 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 GTP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JSY RELATED DB: PDB REMARK 900 RELATED ID: 4JT2 RELATED DB: PDB REMARK 900 RELATED ID: 4JT4 RELATED DB: PDB REMARK 900 RELATED ID: 4JST RELATED DB: PDB REMARK 900 RELATED ID: 4GP6 RELATED DB: PDB REMARK 900 RELATED ID: 4GP7 RELATED DB: PDB REMARK 900 RELATED ID: 4MDE RELATED DB: PDB DBREF 4MDF A 1 170 UNP A3DJ38 A3DJ38_CLOTH 1 170 DBREF 4MDF B 1 170 UNP A3DJ38 A3DJ38_CLOTH 1 170 DBREF 4MDF C 1 5 PDB 4MDF 4MDF 1 5 DBREF 4MDF D 1 5 PDB 4MDF 4MDF 1 5 SEQADV 4MDF SER A 0 UNP A3DJ38 EXPRESSION TAG SEQADV 4MDF ASN A 38 UNP A3DJ38 ASP 38 ENGINEERED MUTATION SEQADV 4MDF MET A 137 UNP A3DJ38 LEU 137 ENGINEERED MUTATION SEQADV 4MDF SER B 0 UNP A3DJ38 EXPRESSION TAG SEQADV 4MDF ASN B 38 UNP A3DJ38 ASP 38 ENGINEERED MUTATION SEQADV 4MDF MET B 137 UNP A3DJ38 LEU 137 ENGINEERED MUTATION SEQRES 1 A 171 SER MET LYS LEU THR ILE PRO GLU LEU SER LEU VAL VAL SEQRES 2 A 171 LEU ILE GLY SER SER GLY SER GLY LYS SER THR PHE ALA SEQRES 3 A 171 LYS LYS HIS PHE LYS PRO THR GLU VAL ILE SER SER ASN SEQRES 4 A 171 PHE CYS ARG GLY LEU VAL SER ASP ASP GLU ASN ASP GLN SEQRES 5 A 171 THR VAL THR GLY ALA ALA PHE ASP VAL LEU HIS TYR ILE SEQRES 6 A 171 VAL SER LYS ARG LEU GLN LEU GLY LYS LEU THR VAL VAL SEQRES 7 A 171 ASP ALA THR ASN VAL GLN GLU SER ALA ARG LYS PRO LEU SEQRES 8 A 171 ILE GLU ILE ALA LYS ASP TYR HIS CYS PHE PRO VAL ALA SEQRES 9 A 171 VAL VAL PHE ASN LEU PRO GLU LYS VAL CYS GLN GLU ARG SEQRES 10 A 171 ASN LYS ASN ARG THR ASP ARG GLN VAL GLU GLU TYR VAL SEQRES 11 A 171 ILE ARG LYS HIS THR GLN GLN MET LYS LYS SER ILE LYS SEQRES 12 A 171 GLY LEU GLN ARG GLU GLY PHE ARG TYR VAL TYR ILE LEU SEQRES 13 A 171 ASN SER PRO GLU GLU VAL GLU GLU VAL VAL PHE GLU ARG SEQRES 14 A 171 GLN PRO SEQRES 1 B 171 SER MET LYS LEU THR ILE PRO GLU LEU SER LEU VAL VAL SEQRES 2 B 171 LEU ILE GLY SER SER GLY SER GLY LYS SER THR PHE ALA SEQRES 3 B 171 LYS LYS HIS PHE LYS PRO THR GLU VAL ILE SER SER ASN SEQRES 4 B 171 PHE CYS ARG GLY LEU VAL SER ASP ASP GLU ASN ASP GLN SEQRES 5 B 171 THR VAL THR GLY ALA ALA PHE ASP VAL LEU HIS TYR ILE SEQRES 6 B 171 VAL SER LYS ARG LEU GLN LEU GLY LYS LEU THR VAL VAL SEQRES 7 B 171 ASP ALA THR ASN VAL GLN GLU SER ALA ARG LYS PRO LEU SEQRES 8 B 171 ILE GLU ILE ALA LYS ASP TYR HIS CYS PHE PRO VAL ALA SEQRES 9 B 171 VAL VAL PHE ASN LEU PRO GLU LYS VAL CYS GLN GLU ARG SEQRES 10 B 171 ASN LYS ASN ARG THR ASP ARG GLN VAL GLU GLU TYR VAL SEQRES 11 B 171 ILE ARG LYS HIS THR GLN GLN MET LYS LYS SER ILE LYS SEQRES 12 B 171 GLY LEU GLN ARG GLU GLY PHE ARG TYR VAL TYR ILE LEU SEQRES 13 B 171 ASN SER PRO GLU GLU VAL GLU GLU VAL VAL PHE GLU ARG SEQRES 14 B 171 GLN PRO SEQRES 1 C 5 DC DC DT DG DT SEQRES 1 D 5 DC DC DT DG DT HET GTP A1001 32 HET MG A1002 1 HET CIT A1003 13 HET GTP B1001 32 HET MG B1002 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CIT CITRIC ACID FORMUL 5 GTP 2(C10 H16 N5 O14 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 CIT C6 H8 O7 FORMUL 10 HOH *395(H2 O) HELIX 1 1 GLY A 20 PHE A 29 1 10 HELIX 2 2 LYS A 30 THR A 32 5 3 HELIX 3 3 SER A 37 ASP A 46 1 10 HELIX 4 4 ASP A 50 THR A 52 5 3 HELIX 5 5 VAL A 53 LEU A 71 1 19 HELIX 6 6 GLN A 83 TYR A 97 1 15 HELIX 7 7 PRO A 109 ARG A 120 1 12 HELIX 8 8 GLU A 126 ILE A 141 1 16 HELIX 9 9 GLY A 143 GLY A 148 1 6 HELIX 10 10 SER A 157 GLU A 163 1 7 HELIX 11 11 GLY B 20 PHE B 29 1 10 HELIX 12 12 LYS B 30 THR B 32 5 3 HELIX 13 13 SER B 37 ASP B 46 1 10 HELIX 14 14 ASP B 50 THR B 52 5 3 HELIX 15 15 VAL B 53 LEU B 71 1 19 HELIX 16 16 GLN B 83 TYR B 97 1 15 HELIX 17 17 PRO B 109 ARG B 120 1 12 HELIX 18 18 GLU B 126 ILE B 141 1 16 HELIX 19 19 GLY B 143 GLY B 148 1 6 HELIX 20 20 SER B 157 GLU B 163 1 7 SHEET 1 A 2 MET A 1 PRO A 6 0 SHEET 2 A 2 VAL A 164 GLN A 169 1 O GLU A 167 N LEU A 3 SHEET 1 B 5 VAL A 34 SER A 36 0 SHEET 2 B 5 THR A 75 ASP A 78 1 O VAL A 76 N ILE A 35 SHEET 3 B 5 SER A 9 ILE A 14 1 N VAL A 11 O VAL A 77 SHEET 4 B 5 PHE A 100 PHE A 106 1 O VAL A 102 N VAL A 12 SHEET 5 B 5 TYR A 151 LEU A 155 1 O LEU A 155 N VAL A 105 SHEET 1 C 2 MET B 1 PRO B 6 0 SHEET 2 C 2 VAL B 164 GLN B 169 1 O GLU B 167 N LEU B 3 SHEET 1 D 5 VAL B 34 SER B 36 0 SHEET 2 D 5 THR B 75 ASP B 78 1 O VAL B 76 N ILE B 35 SHEET 3 D 5 SER B 9 ILE B 14 1 N VAL B 11 O VAL B 77 SHEET 4 D 5 PHE B 100 PHE B 106 1 O VAL B 102 N VAL B 12 SHEET 5 D 5 TYR B 151 LEU B 155 1 O LEU B 155 N VAL B 105 LINK OG SER A 22 MG MG A1002 1555 1555 2.09 LINK O1B GTP A1001 MG MG A1002 1555 1555 2.06 LINK O3G GTP A1001 MG MG A1002 1555 1555 2.08 LINK MG MG A1002 O HOH A1101 1555 1555 2.12 LINK MG MG A1002 O HOH A1102 1555 1555 2.16 LINK MG MG A1002 O HOH A1103 1555 1555 2.11 LINK OG SER B 22 MG MG B1002 1555 1555 2.09 LINK O3G GTP B1001 MG MG B1002 1555 1555 2.05 LINK O1B GTP B1001 MG MG B1002 1555 1555 2.10 LINK MG MG B1002 O HOH B1101 1555 1555 2.06 LINK MG MG B1002 O HOH B1102 1555 1555 2.14 LINK MG MG B1002 O HOH B1103 1555 1555 2.14 SITE 1 AC1 21 SER A 16 SER A 17 GLY A 18 SER A 19 SITE 2 AC1 21 GLY A 20 LYS A 21 SER A 22 THR A 23 SITE 3 AC1 21 ASN A 38 ARG A 116 ARG A 120 ARG A 123 SITE 4 AC1 21 MG A1002 HOH A1101 HOH A1102 HOH A1103 SITE 5 AC1 21 HOH A1155 HOH A1156 HOH A1186 HOH A1211 SITE 6 AC1 21 DC C 1 SITE 1 AC2 5 SER A 22 GTP A1001 HOH A1101 HOH A1102 SITE 2 AC2 5 HOH A1103 SITE 1 AC3 12 HIS A 62 TYR A 63 SER A 66 GLU A 92 SITE 2 AC3 12 ILE A 93 HOH A1151 HOH A1167 HOH A1231 SITE 3 AC3 12 HOH A1243 HOH A1271 DG C 4 DT C 5 SITE 1 AC4 21 SER B 16 SER B 17 GLY B 18 SER B 19 SITE 2 AC4 21 GLY B 20 LYS B 21 SER B 22 THR B 23 SITE 3 AC4 21 ASN B 38 ARG B 116 ARG B 120 ARG B 123 SITE 4 AC4 21 MG B1002 HOH B1101 HOH B1102 HOH B1103 SITE 5 AC4 21 HOH B1149 HOH B1169 HOH B1197 HOH B1200 SITE 6 AC4 21 DC D 1 SITE 1 AC5 5 SER B 22 GTP B1001 HOH B1101 HOH B1102 SITE 2 AC5 5 HOH B1103 CRYST1 53.025 72.755 119.460 90.00 90.00 90.00 P 21 21 21 8 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 0.018859 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008371 0.00000