HEADER TRANSFERASE 17-NOV-21 7QAZ TITLE PRIM-POL DOMAIN OF CRISPR-ASSOCIATED PRIM-POL (CAPP) FROM MARINITOGA TITLE 2 SP. 1137 - PRIMER INITIATION COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TPR_REGION DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TEMPLATING STRAND; COMPND 7 CHAIN: D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARINITOGA SP. 1137; SOURCE 3 ORGANISM_TAXID: 1545835; SOURCE 4 GENE: MARPI_0402; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: POPINF; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS AEP, PRIM-POL, PRIMASE-POLYMERASE, PRIMASE, POLYMERASE, COMPLEX, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.W.H.LI,A.J.DOHERTY REVDAT 6 31-JAN-24 7QAZ 1 REMARK REVDAT 5 02-NOV-22 7QAZ 1 REMARK REVDAT 4 08-JUN-22 7QAZ 1 JRNL REVDAT 3 25-MAY-22 7QAZ 1 SEQADV REVDAT 2 18-MAY-22 7QAZ 1 JRNL REVDAT 1 04-MAY-22 7QAZ 0 JRNL AUTH A.W.H.LI,K.ZABRADY,L.J.BAINBRIDGE,M.ZABRADY,S.NASEEM-KHAN, JRNL AUTH 2 M.B.BERGER,P.KOLESAR,G.A.CISNEROS,A.J.DOHERTY JRNL TITL MOLECULAR BASIS FOR THE INITIATION OF DNA PRIMER SYNTHESIS. JRNL REF NATURE V. 605 767 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35508653 JRNL DOI 10.1038/S41586-022-04695-0 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 40271 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1983 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 56.9800 - 5.0800 0.99 3095 183 0.1904 0.2373 REMARK 3 2 5.0800 - 4.0400 0.99 2934 157 0.1542 0.2070 REMARK 3 3 4.0400 - 3.5300 0.99 2929 157 0.1742 0.2309 REMARK 3 4 3.5300 - 3.2000 1.00 2920 140 0.1981 0.2568 REMARK 3 5 3.2000 - 2.9700 0.99 2890 136 0.2082 0.2501 REMARK 3 6 2.9700 - 2.8000 1.00 2857 174 0.2281 0.2888 REMARK 3 7 2.8000 - 2.6600 0.99 2840 154 0.2257 0.2737 REMARK 3 8 2.6600 - 2.5400 1.00 2874 155 0.2402 0.2841 REMARK 3 9 2.5400 - 2.4400 1.00 2868 141 0.2496 0.3158 REMARK 3 10 2.4400 - 2.3600 0.99 2846 129 0.2743 0.3361 REMARK 3 11 2.3600 - 2.2900 0.92 2643 132 0.2863 0.3143 REMARK 3 12 2.2900 - 2.2200 0.84 2365 126 0.2928 0.3226 REMARK 3 13 2.2200 - 2.1600 0.78 2233 104 0.3181 0.4119 REMARK 3 14 2.1600 - 2.1100 0.70 1994 95 0.3361 0.3578 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) : 0.285 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.481 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.36 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.56 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 : 0.007 5978 REMARK 3 ANGLE : 0.979 8115 REMARK 3 CHIRALITY : 0.057 848 REMARK 3 PLANARITY : 0.008 992 REMARK 3 DIHEDRAL : 20.535 2256 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 7QAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1292119255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 3.4.2 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40376 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 REMARK 200 RESOLUTION RANGE LOW (A) : 56.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 1.04200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 7NQE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM HEPES; MOPS (ACID) 20% V/V REMARK 280 ETHYLENE GLYCOL; 10% W/V PEG 8000 0.03M DIETHYLENE GLYCOL; 0.03M REMARK 280 TRIETHYLENE GLYCOL; 0.03M TETRAETHYLENE GLYCOL; 0.03M REMARK 280 PENTAETHYLENE GLYCOL 400UM DNA; 500UM AMPNPP; 4MM GTP; 2MM COCL2; REMARK 280 130MM MONOPOTASSIUM GLUTAMATE, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 287.15K 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 113.95500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.88500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.81000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.88500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 113.95500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.81000 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, 3 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 APPLY THE FOLLOWING TO CHAINS: B, 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 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 328 REMARK 465 GLY C 110 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 LYS B 190 CG CD CE NZ REMARK 470 LYS C 117 CG CD CE NZ REMARK 470 LYS C 182 CG CD CE NZ REMARK 470 LYS C 246 CG CD CE NZ REMARK 470 LYS C 320 CG CD CE NZ REMARK 470 ARG C 323 CG CD NE CZ NH1 NH2 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 535 O HOH B 581 2.09 REMARK 500 O HOH B 597 O HOH B 622 2.13 REMARK 500 O HOH C 588 O HOH C 597 2.13 REMARK 500 O HOH C 531 O HOH C 599 2.15 REMARK 500 OD2 ASP A 179 O HOH A 501 2.17 REMARK 500 O HOH C 622 O HOH C 623 2.18 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 B 568 O HOH C 617 3544 2.08 REMARK 500 O HOH B 542 O HOH B 629 1545 2.17 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 DA D 1 P DA D 1 OP3 -0.123 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 PHE A 123 47.32 -94.31 REMARK 500 TYR A 134 -169.51 -127.64 REMARK 500 ASP A 189 30.09 -97.39 REMARK 500 ASN A 222 -68.61 -142.83 REMARK 500 ARG A 223 16.68 -142.77 REMARK 500 LYS A 264 -60.49 -96.16 REMARK 500 PHE B 123 53.65 -93.63 REMARK 500 TYR B 134 -169.55 -123.39 REMARK 500 ASP B 189 39.08 -96.69 REMARK 500 ASP B 189 39.08 -94.36 REMARK 500 ASN B 222 -85.97 -147.54 REMARK 500 ASN B 327 12.56 59.39 REMARK 500 PHE C 123 52.31 -92.30 REMARK 500 ASN C 222 -83.39 -155.82 REMARK 500 LEU C 253 -149.68 -93.79 REMARK 500 ASN C 327 50.56 -90.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 630 DISTANCE = 5.97 ANGSTROMS 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 CO A 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 177 OD1 REMARK 620 2 ASP A 177 OD2 50.4 REMARK 620 3 ASP A 179 OD1 100.6 111.7 REMARK 620 4 DZ4 A 402 O2B 87.8 84.6 163.5 REMARK 620 5 DZ4 A 402 O3G 152.0 156.5 77.0 88.9 REMARK 620 6 DZ4 A 402 O1A 131.6 81.3 93.7 91.2 76.3 REMARK 620 7 HOH A 521 O 72.7 123.0 78.5 90.6 79.5 155.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 177 OD2 REMARK 620 2 ASP B 179 OD2 91.8 REMARK 620 3 GLU B 260 OE1 93.7 151.8 REMARK 620 4 DZ4 B 404 O1A 85.3 70.3 137.8 REMARK 620 5 GTP B 405 O3' 138.7 110.2 82.9 71.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 402 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 177 OD1 REMARK 620 2 ASP B 179 OD1 92.1 REMARK 620 3 DZ4 B 404 O2B 92.0 164.5 REMARK 620 4 DZ4 B 404 O1G 154.4 82.3 87.6 REMARK 620 5 DZ4 B 404 O1A 124.1 105.3 84.6 81.3 REMARK 620 6 HOH B 530 O 71.5 69.3 97.9 83.2 164.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 403 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 296 OD1 REMARK 620 2 GLU B 328 OXT 108.8 REMARK 620 3 DZ4 B 406 O3G 124.3 27.7 REMARK 620 4 DZ4 B 406 O1A 99.3 106.0 80.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO D 101 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP B 405 O2B REMARK 620 2 GTP B 405 N7 84.7 REMARK 620 3 HOH B 510 O 91.9 58.8 REMARK 620 4 HOH B 617 O 98.1 161.4 138.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO C 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 177 OD2 REMARK 620 2 ASP C 179 OD2 97.8 REMARK 620 3 GLU C 260 OE1 85.9 132.1 REMARK 620 4 DZ4 C 403 O2A 78.8 85.6 141.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO C 402 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 177 OD1 REMARK 620 2 ASP C 179 OD1 89.2 REMARK 620 3 DZ4 C 403 O2B 92.5 175.6 REMARK 620 4 DZ4 C 403 O2A 110.5 101.3 81.9 REMARK 620 5 DZ4 C 403 O3G 167.7 89.3 88.3 81.8 REMARK 620 6 HOH C 529 O 82.8 86.0 90.2 164.8 84.9 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7NQD RELATED DB: PDB REMARK 900 APO REMARK 900 RELATED ID: 7NQE RELATED DB: PDB REMARK 900 DGTP-BOUND COMPLEX REMARK 900 RELATED ID: 7NQF RELATED DB: PDB REMARK 900 POST-TERNARY COMPLEX REMARK 900 RELATED ID: 7P9J RELATED DB: PDB REMARK 900 PRIMING INITIATION COMPLEX DBREF 7QAZ A 110 328 UNP H2J4R1 H2J4R1_MARPK 110 328 DBREF 7QAZ B 110 328 UNP H2J4R1 H2J4R1_MARPK 110 328 DBREF 7QAZ C 110 328 UNP H2J4R1 H2J4R1_MARPK 110 328 DBREF 7QAZ D 1 9 PDB 7QAZ 7QAZ 1 9 SEQADV 7QAZ GLY A 110 UNP H2J4R1 ALA 110 VARIANT SEQADV 7QAZ GLN A 148 UNP H2J4R1 HIS 148 VARIANT SEQADV 7QAZ ASN A 152 UNP H2J4R1 ASP 152 VARIANT SEQADV 7QAZ THR A 214 UNP H2J4R1 ILE 214 VARIANT SEQADV 7QAZ ASN A 319 UNP H2J4R1 ASP 319 VARIANT SEQADV 7QAZ GLY B 110 UNP H2J4R1 ALA 110 VARIANT SEQADV 7QAZ GLN B 148 UNP H2J4R1 HIS 148 VARIANT SEQADV 7QAZ ASN B 152 UNP H2J4R1 ASP 152 VARIANT SEQADV 7QAZ THR B 214 UNP H2J4R1 ILE 214 VARIANT SEQADV 7QAZ ASN B 319 UNP H2J4R1 ASP 319 VARIANT SEQADV 7QAZ GLY C 110 UNP H2J4R1 ALA 110 VARIANT SEQADV 7QAZ GLN C 148 UNP H2J4R1 HIS 148 VARIANT SEQADV 7QAZ ASN C 152 UNP H2J4R1 ASP 152 VARIANT SEQADV 7QAZ THR C 214 UNP H2J4R1 ILE 214 VARIANT SEQADV 7QAZ ASN C 319 UNP H2J4R1 ASP 319 VARIANT SEQRES 1 A 219 GLY PRO SER GLN ASN ALA ILE LYS ARG PHE MET THR LEU SEQRES 2 A 219 PHE SER GLY ARG GLU ASP VAL PHE SER ILE GLN TYR GLU SEQRES 3 A 219 GLY GLY TYR ARG PRO ILE ARG ARG PRO LEU ASN PHE GLN SEQRES 4 A 219 ASP ILE LYS ASN HIS PHE SER GLY LYS LYS THR LEU GLY SEQRES 5 A 219 ILE TYR LEU LEU LYS LYS ASN ASP THR VAL LYS PHE ALA SEQRES 6 A 219 ALA TYR ASP ILE ASP ILE LYS LYS HIS TYR LEU ASN ARG SEQRES 7 A 219 GLU ASP LYS PHE VAL TYR GLU GLU ASN SER LYS LYS VAL SEQRES 8 A 219 ALA LYS ARG LEU SER ARG GLU LEU ASN LEU GLU ASN ILE SEQRES 9 A 219 THR HIS TYR PHE GLU PHE THR GLY ASN ARG GLY TYR HIS SEQRES 10 A 219 ILE TRP ILE PHE PHE ASP ILE PRO VAL SER ALA TYR LYS SEQRES 11 A 219 ILE LYS TYR ILE MET GLU LYS ILE LEU ASP ARG ILE GLU SEQRES 12 A 219 LEU GLU GLU GLY ILE ASP VAL GLU ILE PHE PRO LYS GLN SEQRES 13 A 219 THR SER LEU ASN GLY GLY LEU GLY ASN LEU ILE LYS VAL SEQRES 14 A 219 PRO LEU GLY VAL HIS LYS LYS THR GLY LYS LYS CYS LEU SEQRES 15 A 219 PHE VAL ASP ASN ASP PHE ASN VAL ILE GLU ASN GLN ILE SEQRES 16 A 219 GLU PHE LEU ASN ASN ILE LYS GLU ASN LYS ALA THR GLU SEQRES 17 A 219 ILE ASN LYS LEU PHE ARG GLU ILE PHE ASN GLU SEQRES 1 B 219 GLY PRO SER GLN ASN ALA ILE LYS ARG PHE MET THR LEU SEQRES 2 B 219 PHE SER GLY ARG GLU ASP VAL PHE SER ILE GLN TYR GLU SEQRES 3 B 219 GLY GLY TYR ARG PRO ILE ARG ARG PRO LEU ASN PHE GLN SEQRES 4 B 219 ASP ILE LYS ASN HIS PHE SER GLY LYS LYS THR LEU GLY SEQRES 5 B 219 ILE TYR LEU LEU LYS LYS ASN ASP THR VAL LYS PHE ALA SEQRES 6 B 219 ALA TYR ASP ILE ASP ILE LYS LYS HIS TYR LEU ASN ARG SEQRES 7 B 219 GLU ASP LYS PHE VAL TYR GLU GLU ASN SER LYS LYS VAL SEQRES 8 B 219 ALA LYS ARG LEU SER ARG GLU LEU ASN LEU GLU ASN ILE SEQRES 9 B 219 THR HIS TYR PHE GLU PHE THR GLY ASN ARG GLY TYR HIS SEQRES 10 B 219 ILE TRP ILE PHE PHE ASP ILE PRO VAL SER ALA TYR LYS SEQRES 11 B 219 ILE LYS TYR ILE MET GLU LYS ILE LEU ASP ARG ILE GLU SEQRES 12 B 219 LEU GLU GLU GLY ILE ASP VAL GLU ILE PHE PRO LYS GLN SEQRES 13 B 219 THR SER LEU ASN GLY GLY LEU GLY ASN LEU ILE LYS VAL SEQRES 14 B 219 PRO LEU GLY VAL HIS LYS LYS THR GLY LYS LYS CYS LEU SEQRES 15 B 219 PHE VAL ASP ASN ASP PHE ASN VAL ILE GLU ASN GLN ILE SEQRES 16 B 219 GLU PHE LEU ASN ASN ILE LYS GLU ASN LYS ALA THR GLU SEQRES 17 B 219 ILE ASN LYS LEU PHE ARG GLU ILE PHE ASN GLU SEQRES 1 C 219 GLY PRO SER GLN ASN ALA ILE LYS ARG PHE MET THR LEU SEQRES 2 C 219 PHE SER GLY ARG GLU ASP VAL PHE SER ILE GLN TYR GLU SEQRES 3 C 219 GLY GLY TYR ARG PRO ILE ARG ARG PRO LEU ASN PHE GLN SEQRES 4 C 219 ASP ILE LYS ASN HIS PHE SER GLY LYS LYS THR LEU GLY SEQRES 5 C 219 ILE TYR LEU LEU LYS LYS ASN ASP THR VAL LYS PHE ALA SEQRES 6 C 219 ALA TYR ASP ILE ASP ILE LYS LYS HIS TYR LEU ASN ARG SEQRES 7 C 219 GLU ASP LYS PHE VAL TYR GLU GLU ASN SER LYS LYS VAL SEQRES 8 C 219 ALA LYS ARG LEU SER ARG GLU LEU ASN LEU GLU ASN ILE SEQRES 9 C 219 THR HIS TYR PHE GLU PHE THR GLY ASN ARG GLY TYR HIS SEQRES 10 C 219 ILE TRP ILE PHE PHE ASP ILE PRO VAL SER ALA TYR LYS SEQRES 11 C 219 ILE LYS TYR ILE MET GLU LYS ILE LEU ASP ARG ILE GLU SEQRES 12 C 219 LEU GLU GLU GLY ILE ASP VAL GLU ILE PHE PRO LYS GLN SEQRES 13 C 219 THR SER LEU ASN GLY GLY LEU GLY ASN LEU ILE LYS VAL SEQRES 14 C 219 PRO LEU GLY VAL HIS LYS LYS THR GLY LYS LYS CYS LEU SEQRES 15 C 219 PHE VAL ASP ASN ASP PHE ASN VAL ILE GLU ASN GLN ILE SEQRES 16 C 219 GLU PHE LEU ASN ASN ILE LYS GLU ASN LYS ALA THR GLU SEQRES 17 C 219 ILE ASN LYS LEU PHE ARG GLU ILE PHE ASN GLU SEQRES 1 D 9 DA DA DA DA DA DT DC DA DA HET CO A 401 1 HET DZ4 A 402 30 HET CO B 401 1 HET CO B 402 1 HET CO B 403 1 HET DZ4 B 404 30 HET GTP B 405 32 HET DZ4 B 406 30 HET CO C 401 1 HET CO C 402 1 HET DZ4 C 403 30 HET CO D 101 1 HETNAM CO COBALT (II) ION HETNAM DZ4 2'-DEOXY-5'-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY) HETNAM 2 DZ4 PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 5 CO 7(CO 2+) FORMUL 6 DZ4 4(C10 H17 N6 O11 P3) FORMUL 11 GTP C10 H16 N5 O14 P3 FORMUL 17 HOH *395(H2 O) HELIX 1 AA1 SER A 112 PHE A 123 1 12 HELIX 2 AA2 ASN A 146 SER A 155 1 10 HELIX 3 AA3 LYS A 182 LEU A 185 5 4 HELIX 4 AA4 ASP A 189 GLU A 211 1 23 HELIX 5 AA5 ALA A 237 ASP A 249 1 13 HELIX 6 AA6 ASN A 302 ILE A 310 1 9 HELIX 7 AA7 LYS A 314 ASN A 327 1 14 HELIX 8 AA8 PRO B 111 PHE B 123 1 13 HELIX 9 AA9 ASN B 146 SER B 155 1 10 HELIX 10 AB1 LYS B 182 LEU B 185 5 4 HELIX 11 AB2 ASP B 189 GLU B 211 1 23 HELIX 12 AB3 ALA B 237 ASP B 249 1 13 HELIX 13 AB4 ASN B 302 ILE B 310 1 9 HELIX 14 AB5 LYS B 314 ASN B 327 1 14 HELIX 15 AB6 SER C 112 PHE C 123 1 12 HELIX 16 AB7 ASN C 146 SER C 155 1 10 HELIX 17 AB8 LYS C 181 ASN C 186 1 6 HELIX 18 AB9 ASP C 189 GLU C 211 1 23 HELIX 19 AC1 ALA C 237 ILE C 251 1 15 HELIX 20 AC2 ASN C 302 ASN C 309 1 8 HELIX 21 AC3 LYS C 314 ASN C 327 1 14 SHEET 1 AA1 4 GLY A 137 ILE A 141 0 SHEET 2 AA1 4 PHE A 130 TYR A 134 -1 N PHE A 130 O ILE A 141 SHEET 3 AA1 4 LEU A 160 TYR A 163 -1 O GLY A 161 N SER A 131 SHEET 4 AA1 4 LEU A 275 LYS A 277 -1 O ILE A 276 N ILE A 162 SHEET 1 AA2 5 ILE A 257 PHE A 262 0 SHEET 2 AA2 5 THR A 170 ILE A 180 -1 N ASP A 177 O GLU A 260 SHEET 3 AA2 5 GLY A 224 SER A 236 -1 O ILE A 229 N ALA A 174 SHEET 4 AA2 5 HIS A 215 PHE A 219 -1 N TYR A 216 O TRP A 228 SHEET 5 AA2 5 LEU A 291 VAL A 293 -1 O LEU A 291 N PHE A 219 SHEET 1 AA3 4 GLY B 137 ILE B 141 0 SHEET 2 AA3 4 PHE B 130 TYR B 134 -1 N PHE B 130 O ILE B 141 SHEET 3 AA3 4 LEU B 160 TYR B 163 -1 O GLY B 161 N SER B 131 SHEET 4 AA3 4 LEU B 275 LYS B 277 -1 O ILE B 276 N ILE B 162 SHEET 1 AA4 5 ILE B 257 PHE B 262 0 SHEET 2 AA4 5 THR B 170 ILE B 180 -1 N ALA B 175 O PHE B 262 SHEET 3 AA4 5 GLY B 224 SER B 236 -1 O VAL B 235 N VAL B 171 SHEET 4 AA4 5 HIS B 215 PHE B 219 -1 N TYR B 216 O TRP B 228 SHEET 5 AA4 5 LEU B 291 VAL B 293 -1 O LEU B 291 N PHE B 219 SHEET 1 AA5 4 GLY C 137 ILE C 141 0 SHEET 2 AA5 4 PHE C 130 TYR C 134 -1 N PHE C 130 O ILE C 141 SHEET 3 AA5 4 LEU C 160 TYR C 163 -1 O GLY C 161 N SER C 131 SHEET 4 AA5 4 LEU C 275 LYS C 277 -1 O ILE C 276 N ILE C 162 SHEET 1 AA6 5 ILE C 257 PHE C 262 0 SHEET 2 AA6 5 THR C 170 ILE C 180 -1 N ASP C 179 O ASP C 258 SHEET 3 AA6 5 GLY C 224 SER C 236 -1 O TYR C 225 N ILE C 178 SHEET 4 AA6 5 TYR C 216 PHE C 219 -1 N TYR C 216 O TRP C 228 SHEET 5 AA6 5 LEU C 291 VAL C 293 -1 O LEU C 291 N PHE C 219 LINK OD1 ASP A 177 CO CO A 401 1555 1555 2.39 LINK OD2 ASP A 177 CO CO A 401 1555 1555 2.77 LINK OD1 ASP A 179 CO CO A 401 1555 1555 2.36 LINK CO CO A 401 O2B DZ4 A 402 1555 1555 2.15 LINK CO CO A 401 O3G DZ4 A 402 1555 1555 2.28 LINK CO CO A 401 O1A DZ4 A 402 1555 1555 2.22 LINK CO CO A 401 O HOH A 521 1555 1555 1.86 LINK OD2 ASP B 177 CO CO B 401 1555 1555 2.26 LINK OD1 ASP B 177 CO CO B 402 1555 1555 2.47 LINK OD2 ASP B 179 CO CO B 401 1555 1555 2.20 LINK OD1 ASP B 179 CO CO B 402 1555 1555 2.23 LINK OE1 GLU B 260 CO CO B 401 1555 1555 2.67 LINK OD1 ASP B 296 CO CO B 403 1555 1555 2.23 LINK OXT GLU B 328 CO CO B 403 1555 1545 2.78 LINK CO CO B 401 O1A DZ4 B 404 1555 1555 2.65 LINK CO CO B 401 O3' GTP B 405 1555 1555 2.10 LINK CO CO B 402 O2B DZ4 B 404 1555 1555 2.23 LINK CO CO B 402 O1G DZ4 B 404 1555 1555 2.08 LINK CO CO B 402 O1A DZ4 B 404 1555 1555 2.47 LINK CO CO B 402 O HOH B 530 1555 1555 2.51 LINK CO CO B 403 O3G DZ4 B 406 1555 1555 2.57 LINK CO CO B 403 O1A DZ4 B 406 1555 1555 2.80 LINK O2B GTP B 405 CO CO D 101 1555 1555 2.22 LINK N7 GTP B 405 CO CO D 101 1555 1555 2.45 LINK O HOH B 510 CO CO D 101 1555 1555 2.59 LINK O HOH B 617 CO CO D 101 1555 1555 2.21 LINK OD2 ASP C 177 CO CO C 401 1555 1555 2.22 LINK OD1 ASP C 177 CO CO C 402 1555 1555 2.14 LINK OD2 ASP C 179 CO CO C 401 1555 1555 1.92 LINK OD1 ASP C 179 CO CO C 402 1555 1555 1.93 LINK OE1 GLU C 260 CO CO C 401 1555 1555 2.72 LINK CO CO C 401 O2A DZ4 C 403 1555 1555 2.36 LINK CO CO C 402 O2B DZ4 C 403 1555 1555 2.03 LINK CO CO C 402 O2A DZ4 C 403 1555 1555 2.05 LINK CO CO C 402 O3G DZ4 C 403 1555 1555 2.18 LINK CO CO C 402 O HOH C 529 1555 1555 2.00 CISPEP 1 PHE A 262 PRO A 263 0 7.17 CISPEP 2 PHE B 262 PRO B 263 0 6.60 CISPEP 3 PHE C 262 PRO C 263 0 0.98 CRYST1 227.910 39.620 79.770 90.00 90.00 90.00 P 21 21 21 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 0.004388 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012536 0.00000