HEADER TRANSFERASE/DNA 22-AUG-13 4MDE TITLE STRUCTURE OF BACTERIAL POLYNUCLEOTIDE KINASE PRODUCT COMPLEX BOUND TO TITLE 2 GDP 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(P*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 4MDE 1 REMARK SEQADV LINK REVDAT 2 12-FEB-14 4MDE 1 JRNL REVDAT 1 06-NOV-13 4MDE 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 43651 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.880 REMARK 3 FREE R VALUE TEST SET COUNT : 3439 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 41.0060 - 5.2597 0.92 1659 147 0.1788 0.2136 REMARK 3 2 5.2597 - 4.1761 0.96 1637 137 0.1432 0.1736 REMARK 3 3 4.1761 - 3.6486 0.98 1637 139 0.1466 0.1792 REMARK 3 4 3.6486 - 3.3152 0.99 1676 139 0.1611 0.1945 REMARK 3 5 3.3152 - 3.0776 0.99 1663 132 0.1679 0.1853 REMARK 3 6 3.0776 - 2.8962 0.98 1618 138 0.1651 0.1901 REMARK 3 7 2.8962 - 2.7512 0.98 1626 149 0.1668 0.1884 REMARK 3 8 2.7512 - 2.6315 0.98 1592 147 0.1628 0.2185 REMARK 3 9 2.6315 - 2.5302 0.99 1633 129 0.1755 0.2114 REMARK 3 10 2.5302 - 2.4429 0.97 1600 151 0.1668 0.2327 REMARK 3 11 2.4429 - 2.3665 0.98 1607 119 0.1653 0.2350 REMARK 3 12 2.3665 - 2.2989 0.98 1621 139 0.1625 0.2292 REMARK 3 13 2.2989 - 2.2384 0.96 1578 140 0.1600 0.2374 REMARK 3 14 2.2384 - 2.1838 0.98 1588 136 0.1632 0.2155 REMARK 3 15 2.1838 - 2.1341 0.97 1601 135 0.1563 0.2082 REMARK 3 16 2.1341 - 2.0887 0.98 1564 142 0.1582 0.2156 REMARK 3 17 2.0887 - 2.0469 0.98 1619 140 0.1586 0.1952 REMARK 3 18 2.0469 - 2.0083 0.96 1562 138 0.1687 0.2305 REMARK 3 19 2.0083 - 1.9724 0.98 1587 141 0.1746 0.2242 REMARK 3 20 1.9724 - 1.9390 0.98 1616 113 0.1712 0.2471 REMARK 3 21 1.9390 - 1.9077 0.98 1620 127 0.1759 0.2408 REMARK 3 22 1.9077 - 1.8784 0.97 1539 148 0.1795 0.2035 REMARK 3 23 1.8784 - 1.8507 0.97 1565 146 0.1925 0.2308 REMARK 3 24 1.8507 - 1.8247 0.98 1562 144 0.2063 0.2732 REMARK 3 25 1.8247 - 1.8000 0.98 1642 123 0.2228 0.2708 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.190 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 3089 REMARK 3 ANGLE : 1.084 4226 REMARK 3 CHIRALITY : 0.071 481 REMARK 3 PLANARITY : 0.004 503 REMARK 3 DIHEDRAL : 15.352 1206 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 4MDE 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_1000081770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-AUG-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 : 43723 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 46.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 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 REFINEMENT 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 (%): 56.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM CITRATE, PH 5.0, 2 MM REMARK 280 GUANOSINE DIPHOSPHATE, 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 27.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.52000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.56000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.52000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.56000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -27.22000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 59.52000 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 B 1198 O HOH B 1228 2.16 REMARK 500 O HOH A 1241 O HOH A 1266 2.17 REMARK 500 O HOH A 1196 O HOH A 1251 2.18 REMARK 500 O HOH A 1221 O HOH A 1231 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 DC C 1 P DC C 1 OP3 -0.133 REMARK 500 DC D 1 P DC D 1 OP3 -0.120 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 DC D 1 O4' - C1' - N1 ANGL. DEV. = 2.1 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 -6.53 76.40 REMARK 500 ASP A 122 -145.79 -112.97 REMARK 500 ASP B 46 -8.48 77.08 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 GDP A1001 O1B 93.1 REMARK 620 3 HOH A1101 O 90.0 88.8 REMARK 620 4 HOH A1102 O 80.4 173.0 88.6 REMARK 620 5 HOH A1103 O 85.8 93.1 175.5 89.0 REMARK 620 6 DC C 1 OP3 167.5 97.2 97.3 89.5 86.6 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 GDP B1001 O1B 91.2 REMARK 620 3 HOH B1101 O 89.8 88.2 REMARK 620 4 HOH B1102 O 83.8 174.4 89.2 REMARK 620 5 HOH B1103 O 84.8 94.2 174.2 88.0 REMARK 620 6 DC D 1 OP1 172.1 96.3 92.8 88.7 92.2 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 GDP 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 GDP B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 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: 4MDF RELATED DB: PDB DBREF 4MDE A 1 170 UNP A3DJ38 A3DJ38_CLOTH 1 170 DBREF 4MDE B 1 170 UNP A3DJ38 A3DJ38_CLOTH 1 170 DBREF 4MDE C 1 5 PDB 4MDE 4MDE 1 5 DBREF 4MDE D 1 5 PDB 4MDE 4MDE 1 5 SEQADV 4MDE SER A 0 UNP A3DJ38 EXPRESSION TAG SEQADV 4MDE ASN A 38 UNP A3DJ38 ASP 38 ENGINEERED MUTATION SEQADV 4MDE MET A 137 UNP A3DJ38 LEU 137 ENGINEERED MUTATION SEQADV 4MDE SER B 0 UNP A3DJ38 EXPRESSION TAG SEQADV 4MDE ASN B 38 UNP A3DJ38 ASP 38 ENGINEERED MUTATION SEQADV 4MDE 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 GDP A1001 28 HET MG A1002 1 HET GDP B1001 28 HET MG B1002 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 GDP 2(C10 H15 N5 O11 P2) FORMUL 6 MG 2(MG 2+) FORMUL 9 HOH *440(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 ASN A 119 1 11 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 VAL A 165 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 TYR A 153 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 VAL B 165 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 TYR B 153 N VAL B 105 LINK OG SER A 22 MG MG A1002 1555 1555 2.13 LINK O1B GDP A1001 MG MG A1002 1555 1555 2.01 LINK MG MG A1002 O HOH A1101 1555 1555 2.17 LINK MG MG A1002 O HOH A1102 1555 1555 2.21 LINK MG MG A1002 O HOH A1103 1555 1555 2.11 LINK MG MG A1002 OP3 DC C 1 1555 1555 2.10 LINK OG SER B 22 MG MG B1002 1555 1555 2.09 LINK O1B GDP B1001 MG MG B1002 1555 1555 2.08 LINK MG MG B1002 O HOH B1101 1555 1555 2.09 LINK MG MG B1002 O HOH B1102 1555 1555 2.17 LINK MG MG B1002 O HOH B1103 1555 1555 2.09 LINK MG MG B1002 OP1 DC D 1 1555 1555 2.06 SITE 1 AC1 20 SER A 16 GLY A 18 SER A 19 GLY A 20 SITE 2 AC1 20 LYS A 21 SER A 22 THR A 23 ARG A 116 SITE 3 AC1 20 ARG A 120 ARG A 123 MG A1002 HOH A1101 SITE 4 AC1 20 HOH A1103 HOH A1184 HOH A1191 HOH A1214 SITE 5 AC1 20 HOH A1226 HOH A1259 LYS B 118 DC C 1 SITE 1 AC2 7 SER A 22 ARG A 123 GDP A1001 HOH A1101 SITE 2 AC2 7 HOH A1102 HOH A1103 DC C 1 SITE 1 AC3 18 SER B 16 GLY B 18 SER B 19 GLY B 20 SITE 2 AC3 18 LYS B 21 SER B 22 THR B 23 ARG B 116 SITE 3 AC3 18 ARG B 120 MG B1002 HOH B1101 HOH B1103 SITE 4 AC3 18 HOH B1149 HOH B1189 HOH B1200 HOH B1222 SITE 5 AC3 18 HOH B1248 DC D 1 SITE 1 AC4 7 SER B 22 ARG B 123 GDP B1001 HOH B1101 SITE 2 AC4 7 HOH B1102 HOH B1103 DC D 1 CRYST1 54.440 73.120 119.040 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 0.018369 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013676 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008401 0.00000