HEADER REPLICATION/DNA 05-APR-23 8SCK TITLE BST DNA POLYMERASE I LARGE FRAGMENT MUTANT F710Y/D598A WITH 3'-AMINO TITLE 2 PRIMER, DGTP, AND CALCIUM TIME-RESOLVED 4H COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE I; COMPND 3 CHAIN: A, D; COMPND 4 EC: 2.7.7.7; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA PRIMER/PRODUCT; COMPND 8 CHAIN: B, E; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA TEMPLATE; COMPND 12 CHAIN: C, F; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 1422; SOURCE 4 GENE: DPO1, POLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630 KEYWDS DNA POLYMERASE, NP-DNA, ORIGIN OF LIFE, TIME-RESOLVED KEYWDS 2 CRYSTALLOGRAPHY, DNA BINDING PROTEIN, REPLICATION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Z.FANG,V.S.LELYVELD,J.W.SZOSTAK REVDAT 2 08-NOV-23 8SCK 1 JRNL REVDAT 1 25-OCT-23 8SCK 0 JRNL AUTH V.S.LELYVELD,Z.FANG,J.W.SZOSTAK JRNL TITL TRIVALENT RARE EARTH METAL COFACTORS CONFER RAPID NP-DNA JRNL TITL 2 POLYMERASE ACTIVITY. JRNL REF SCIENCE V. 382 423 2023 JRNL REFN ESSN 1095-9203 JRNL PMID 37883544 JRNL DOI 10.1126/SCIENCE.ADH5339 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 66268 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3316 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 39.6300 - 6.6300 0.98 2876 144 0.1548 0.1794 REMARK 3 2 6.6200 - 5.2600 1.00 2792 146 0.1732 0.2077 REMARK 3 3 5.2600 - 4.6000 1.00 2743 153 0.1539 0.2124 REMARK 3 4 4.6000 - 4.1800 1.00 2736 139 0.1553 0.1966 REMARK 3 5 4.1800 - 3.8800 0.71 1914 116 0.1739 0.2014 REMARK 3 6 3.8800 - 3.6500 0.79 2137 119 0.2249 0.2613 REMARK 3 7 3.6500 - 3.4700 0.88 2377 121 0.2076 0.2840 REMARK 3 8 3.4700 - 3.3200 1.00 2693 150 0.1989 0.2426 REMARK 3 9 3.3200 - 3.1900 1.00 2685 148 0.2024 0.2592 REMARK 3 10 3.1900 - 3.0800 1.00 2732 134 0.2142 0.2311 REMARK 3 11 3.0800 - 2.9800 1.00 2671 138 0.2127 0.2892 REMARK 3 12 2.9800 - 2.9000 1.00 2721 120 0.2216 0.2734 REMARK 3 13 2.9000 - 2.8200 1.00 2694 134 0.2163 0.2942 REMARK 3 14 2.8200 - 2.7500 1.00 2664 142 0.2235 0.3144 REMARK 3 15 2.7500 - 2.6900 1.00 2700 138 0.2241 0.2931 REMARK 3 16 2.6900 - 2.6300 1.00 2665 131 0.2217 0.3112 REMARK 3 17 2.6300 - 2.5800 1.00 2658 170 0.2164 0.3036 REMARK 3 18 2.5800 - 2.5300 1.00 2667 132 0.2063 0.2765 REMARK 3 19 2.5300 - 2.4900 1.00 2676 147 0.2074 0.2925 REMARK 3 20 2.4900 - 2.4400 1.00 2670 150 0.2103 0.2700 REMARK 3 21 2.4400 - 2.4000 0.99 2665 143 0.2136 0.2978 REMARK 3 22 2.4000 - 2.3700 0.99 2645 131 0.2094 0.3263 REMARK 3 23 2.3700 - 2.3300 0.99 2650 132 0.2137 0.2818 REMARK 3 24 2.3300 - 2.3000 0.95 2521 138 0.2168 0.2791 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) : 0.282 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.052 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.29 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.62 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 : 0.008 10606 REMARK 3 ANGLE : 0.913 14546 REMARK 3 CHIRALITY : 0.050 1622 REMARK 3 PLANARITY : 0.005 1708 REMARK 3 DIHEDRAL : 17.148 4088 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 8SCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 5.3-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66713 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.43200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULPHATE, 0.1M MES PH 5.3 REMARK 280 -6.0, 20 MM CACL2, 5% MPD, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 46.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 74.67800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.46600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 74.67800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.46600 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 DC C 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC C 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC C 1 C6 REMARK 470 DC F 1 O5' C5' C4' O4' C3' C2' C1' REMARK 470 DC F 1 N1 C2 O2 N3 C4 N4 C5 REMARK 470 DC F 1 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 O3' DGT A 902 O HOH A 1001 2.02 REMARK 500 O6 DPO A 901 O HOH A 1002 2.10 REMARK 500 NE2 GLN A 656 O HOH A 1003 2.12 REMARK 500 O3' DGT D 902 O HOH D 1001 2.16 REMARK 500 O ILE D 528 O HOH D 1002 2.16 REMARK 500 O6 DPO D 901 O HOH D 1003 2.17 REMARK 500 O2B DGT D 902 O HOH D 1003 2.18 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 E 6 O3' DC E 6 C3' -0.046 REMARK 500 DA F 2 O3' DA F 2 C3' -0.040 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 B 6 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG C 4 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT E 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC E 6 O4' - C1' - N1 ANGL. DEV. = 3.0 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 402 96.17 -163.36 REMARK 500 ALA A 421 46.23 -89.36 REMARK 500 LEU A 477 -69.72 -120.75 REMARK 500 HIS A 568 141.98 -172.52 REMARK 500 ILE A 588 -72.20 -99.84 REMARK 500 ILE A 628 -29.09 -149.29 REMARK 500 HIS A 829 -51.30 77.62 REMARK 500 ALA A 875 34.96 -76.70 REMARK 500 LEU D 312 47.57 -107.35 REMARK 500 ASP D 372 65.01 61.36 REMARK 500 ALA D 421 43.32 -89.90 REMARK 500 ILE D 588 -69.62 -100.67 REMARK 500 ILE D 628 -24.60 -150.04 REMARK 500 GLN D 656 60.85 32.33 REMARK 500 ASP D 678 89.74 -34.48 REMARK 500 HIS D 829 -55.69 77.34 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 CA A 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 653 OD2 REMARK 620 2 TYR A 654 O 72.4 REMARK 620 3 ASP A 830 OD2 120.1 77.2 REMARK 620 4 DPO A 901 O2 94.1 106.3 144.2 REMARK 620 5 DPO A 901 O6 147.0 85.0 76.0 69.0 REMARK 620 6 DGT A 902 O2G 96.5 107.2 142.0 2.4 67.0 REMARK 620 7 DGT A 902 O2B 142.2 86.4 83.5 61.6 7.5 59.7 REMARK 620 8 DGT A 902 O2A 153.0 134.6 73.5 80.3 54.8 78.1 56.6 REMARK 620 9 HOH A1051 O 78.3 133.9 88.0 110.7 133.6 110.9 135.5 79.1 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA D 903 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 653 OD2 REMARK 620 2 TYR D 654 O 77.6 REMARK 620 3 ASP D 830 OD2 121.5 90.1 REMARK 620 4 DPO D 901 O2 82.6 99.5 155.6 REMARK 620 5 DPO D 901 O6 147.0 89.9 88.5 69.3 REMARK 620 6 DGT D 902 O2G 85.4 100.7 152.7 2.9 66.8 REMARK 620 7 DGT D 902 O2B 145.5 89.1 89.8 68.1 1.5 65.6 REMARK 620 8 DGT D 902 O2A 132.9 148.8 69.2 92.2 67.2 89.8 68.5 REMARK 620 9 HOH D1003 O 147.4 70.5 53.2 109.0 41.9 106.9 42.7 78.3 REMARK 620 N 1 2 3 4 5 6 7 8 DBREF 8SCK A 298 876 UNP D9N168 D9N168_GEOSE 1 579 DBREF 8SCK B 1 10 PDB 8SCK 8SCK 1 10 DBREF 8SCK C 1 13 PDB 8SCK 8SCK 1 13 DBREF 8SCK D 298 876 UNP D9N168 D9N168_GEOSE 1 579 DBREF 8SCK E 1 10 PDB 8SCK 8SCK 1 10 DBREF 8SCK F 1 13 PDB 8SCK 8SCK 1 13 SEQADV 8SCK TYR A 710 UNP D9N168 PHE 413 ENGINEERED MUTATION SEQADV 8SCK VAL A 713 UNP D9N168 PRO 416 VARIANT SEQADV 8SCK TYR D 710 UNP D9N168 PHE 413 ENGINEERED MUTATION SEQADV 8SCK VAL D 713 UNP D9N168 PRO 416 VARIANT SEQRES 1 A 579 LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU GLU SEQRES 2 A 579 MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL VAL SEQRES 3 A 579 GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE ALA SEQRES 4 A 579 VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO GLU SEQRES 5 A 579 THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU GLY SEQRES 6 A 579 ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS ARG SEQRES 7 A 579 ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU CYS SEQRES 8 A 579 GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU LEU SEQRES 9 A 579 ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA ALA SEQRES 10 A 579 LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU ALA SEQRES 11 A 579 VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP GLU SEQRES 12 A 579 PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA ALA SEQRES 13 A 579 ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU ARG SEQRES 14 A 579 ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU GLN SEQRES 15 A 579 PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA GLY SEQRES 16 A 579 VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY LYS SEQRES 17 A 579 GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG ILE SEQRES 18 A 579 TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER PRO SEQRES 19 A 579 LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN LEU SEQRES 20 A 579 PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SER SEQRES 21 A 579 ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU ILE SEQRES 22 A 579 VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS LEU SEQRES 23 A 579 GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL ARG SEQRES 24 A 579 PRO ALA THR LYS LYS VAL HIS THR ILE PHE ASN GLN ALA SEQRES 25 A 579 LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO ASN SEQRES 26 A 579 LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG LYS SEQRES 27 A 579 ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP LEU SEQRES 28 A 579 ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG VAL SEQRES 29 A 579 LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU ALA SEQRES 30 A 579 PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA MET SEQRES 31 A 579 ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO ASN SEQRES 32 A 579 MET ARG ARG GLN ALA LYS ALA VAL ASN TYR GLY ILE VAL SEQRES 33 A 579 TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU ASN SEQRES 34 A 579 ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG TYR SEQRES 35 A 579 PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU ASN SEQRES 36 A 579 ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR THR SEQRES 37 A 579 LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SER SEQRES 38 A 579 ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET ALA SEQRES 39 A 579 MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE ILE SEQRES 40 A 579 LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS GLU SEQRES 41 A 579 GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS ASP SEQRES 42 A 579 GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU ARG SEQRES 43 A 579 LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA VAL SEQRES 44 A 579 THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR GLY SEQRES 45 A 579 SER THR TRP TYR ASP ALA LYS SEQRES 1 B 10 DG DC DG DA DT DC DA DG C42 DG SEQRES 1 C 13 DC DA DC DG DC DT DG DA DT DC DG DC DA SEQRES 1 D 579 LYS MET ALA PHE THR LEU ALA ASP ARG VAL THR GLU GLU SEQRES 2 D 579 MET LEU ALA ASP LYS ALA ALA LEU VAL VAL GLU VAL VAL SEQRES 3 D 579 GLU GLU ASN TYR HIS ASP ALA PRO ILE VAL GLY ILE ALA SEQRES 4 D 579 VAL VAL ASN GLU HIS GLY ARG PHE PHE LEU ARG PRO GLU SEQRES 5 D 579 THR ALA LEU ALA ASP PRO GLN PHE VAL ALA TRP LEU GLY SEQRES 6 D 579 ASP GLU THR LYS LYS LYS SER MET PHE ASP SER LYS ARG SEQRES 7 D 579 ALA ALA VAL ALA LEU LYS TRP LYS GLY ILE GLU LEU CYS SEQRES 8 D 579 GLY VAL SER PHE ASP LEU LEU LEU ALA ALA TYR LEU LEU SEQRES 9 D 579 ASP PRO ALA GLN GLY VAL ASP ASP VAL ALA ALA ALA ALA SEQRES 10 D 579 LYS MET LYS GLN TYR GLU ALA VAL ARG PRO ASP GLU ALA SEQRES 11 D 579 VAL TYR GLY LYS GLY ALA LYS ARG ALA VAL PRO ASP GLU SEQRES 12 D 579 PRO VAL LEU ALA GLU HIS LEU VAL ARG LYS ALA ALA ALA SEQRES 13 D 579 ILE TRP GLU LEU GLU ARG PRO PHE LEU ASP GLU LEU ARG SEQRES 14 D 579 ARG ASN GLU GLN ASP ARG LEU LEU VAL GLU LEU GLU GLN SEQRES 15 D 579 PRO LEU SER SER ILE LEU ALA GLU MET GLU PHE ALA GLY SEQRES 16 D 579 VAL LYS VAL ASP THR LYS ARG LEU GLU GLN MET GLY LYS SEQRES 17 D 579 GLU LEU ALA GLU GLN LEU GLY THR VAL GLU GLN ARG ILE SEQRES 18 D 579 TYR GLU LEU ALA GLY GLN GLU PHE ASN ILE ASN SER PRO SEQRES 19 D 579 LYS GLN LEU GLY VAL ILE LEU PHE GLU LYS LEU GLN LEU SEQRES 20 D 579 PRO VAL LEU LYS LYS THR LYS THR GLY TYR SER THR SER SEQRES 21 D 579 ALA ASP VAL LEU GLU LYS LEU ALA PRO TYR HIS GLU ILE SEQRES 22 D 579 VAL GLU ASN ILE LEU HIS TYR ARG GLN LEU GLY LYS LEU SEQRES 23 D 579 GLN SER THR TYR ILE GLU GLY LEU LEU LYS VAL VAL ARG SEQRES 24 D 579 PRO ALA THR LYS LYS VAL HIS THR ILE PHE ASN GLN ALA SEQRES 25 D 579 LEU THR GLN THR GLY ARG LEU SER SER THR GLU PRO ASN SEQRES 26 D 579 LEU GLN ASN ILE PRO ILE ARG LEU GLU GLU GLY ARG LYS SEQRES 27 D 579 ILE ARG GLN ALA PHE VAL PRO SER GLU SER ASP TRP LEU SEQRES 28 D 579 ILE PHE ALA ALA ASP TYR SER GLN ILE GLU LEU ARG VAL SEQRES 29 D 579 LEU ALA HIS ILE ALA GLU ASP ASP ASN LEU MET GLU ALA SEQRES 30 D 579 PHE ARG ARG ASP LEU ASP ILE HIS THR LYS THR ALA MET SEQRES 31 D 579 ASP ILE PHE GLN VAL SER GLU ASP GLU VAL THR PRO ASN SEQRES 32 D 579 MET ARG ARG GLN ALA LYS ALA VAL ASN TYR GLY ILE VAL SEQRES 33 D 579 TYR GLY ILE SER ASP TYR GLY LEU ALA GLN ASN LEU ASN SEQRES 34 D 579 ILE SER ARG LYS GLU ALA ALA GLU PHE ILE GLU ARG TYR SEQRES 35 D 579 PHE GLU SER PHE PRO GLY VAL LYS ARG TYR MET GLU ASN SEQRES 36 D 579 ILE VAL GLN GLU ALA LYS GLN LYS GLY TYR VAL THR THR SEQRES 37 D 579 LEU LEU HIS ARG ARG ARG TYR LEU PRO ASP ILE THR SER SEQRES 38 D 579 ARG ASN PHE ASN VAL ARG SER PHE ALA GLU ARG MET ALA SEQRES 39 D 579 MET ASN THR PRO ILE GLN GLY SER ALA ALA ASP ILE ILE SEQRES 40 D 579 LYS LYS ALA MET ILE ASP LEU ASN ALA ARG LEU LYS GLU SEQRES 41 D 579 GLU ARG LEU GLN ALA HIS LEU LEU LEU GLN VAL HIS ASP SEQRES 42 D 579 GLU LEU ILE LEU GLU ALA PRO LYS GLU GLU MET GLU ARG SEQRES 43 D 579 LEU CYS ARG LEU VAL PRO GLU VAL MET GLU GLN ALA VAL SEQRES 44 D 579 THR LEU ARG VAL PRO LEU LYS VAL ASP TYR HIS TYR GLY SEQRES 45 D 579 SER THR TRP TYR ASP ALA LYS SEQRES 1 E 10 DG DC DG DA DT DC DA DG C42 DG SEQRES 1 F 13 DC DA DC DG DC DT DG DA DT DC DG DC DA HET C42 B 9 38 HET C42 E 9 38 HET DPO A 901 9 HET DGT A 902 31 HET CA A 903 1 HET SO4 A 904 5 HET SO4 A 905 5 HET SO4 A 906 5 HET SO4 A 907 5 HET DPO D 901 9 HET DGT D 902 31 HET CA D 903 1 HETNAM C42 3'-AMINO-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM DPO DIPHOSPHATE HETNAM DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION FORMUL 2 C42 2(C9 H15 N4 O6 P) FORMUL 7 DPO 2(O7 P2 4-) FORMUL 8 DGT 2(C10 H16 N5 O13 P3) FORMUL 9 CA 2(CA 2+) FORMUL 10 SO4 4(O4 S 2-) FORMUL 17 HOH *239(H2 O) HELIX 1 AA1 THR A 308 LEU A 312 5 5 HELIX 2 AA2 ARG A 347 LEU A 352 1 6 HELIX 3 AA3 ASP A 354 ASP A 363 1 10 HELIX 4 AA4 ASP A 372 LYS A 383 1 12 HELIX 5 AA5 LEU A 394 ASP A 402 1 9 HELIX 6 AA6 PRO A 403 GLY A 406 5 4 HELIX 7 AA7 ASP A 409 MET A 416 1 8 HELIX 8 AA8 PRO A 424 GLY A 430 1 7 HELIX 9 AA9 LYS A 431 ARG A 435 5 5 HELIX 10 AB1 ASP A 439 ASN A 468 1 30 HELIX 11 AB2 GLN A 470 LEU A 477 1 8 HELIX 12 AB3 LEU A 477 GLY A 492 1 16 HELIX 13 AB4 ASP A 496 ALA A 522 1 27 HELIX 14 AB5 SER A 530 GLU A 540 1 11 HELIX 15 AB6 SER A 557 ALA A 565 1 9 HELIX 16 AB7 GLU A 569 THR A 586 1 18 HELIX 17 AB8 ILE A 588 LYS A 593 1 6 HELIX 18 AB9 LEU A 630 LYS A 635 1 6 HELIX 19 AC1 ILE A 636 GLN A 638 5 3 HELIX 20 AC2 GLN A 656 GLU A 667 1 12 HELIX 21 AC3 ASP A 668 ARG A 677 1 10 HELIX 22 AC4 ASP A 680 PHE A 690 1 11 HELIX 23 AC5 SER A 693 VAL A 697 5 5 HELIX 24 AC6 THR A 698 TYR A 714 1 17 HELIX 25 AC7 SER A 717 ASN A 726 1 10 HELIX 26 AC8 SER A 728 PHE A 743 1 16 HELIX 27 AC9 PHE A 743 GLY A 761 1 19 HELIX 28 AD1 PRO A 774 SER A 778 5 5 HELIX 29 AD2 ASN A 780 GLU A 818 1 39 HELIX 30 AD3 GLU A 840 GLN A 854 1 15 HELIX 31 AD4 THR D 308 LEU D 312 5 5 HELIX 32 AD5 ARG D 347 LEU D 352 1 6 HELIX 33 AD6 ASP D 354 ASP D 363 1 10 HELIX 34 AD7 ASP D 372 LYS D 383 1 12 HELIX 35 AD8 LEU D 394 ASP D 402 1 9 HELIX 36 AD9 PRO D 403 GLY D 406 5 4 HELIX 37 AE1 ASP D 409 MET D 416 1 8 HELIX 38 AE2 PRO D 424 GLY D 430 1 7 HELIX 39 AE3 LYS D 431 ARG D 435 5 5 HELIX 40 AE4 ASP D 439 ASN D 468 1 30 HELIX 41 AE5 GLN D 470 LEU D 477 1 8 HELIX 42 AE6 LEU D 477 GLY D 492 1 16 HELIX 43 AE7 ASP D 496 ALA D 522 1 27 HELIX 44 AE8 SER D 530 GLU D 540 1 11 HELIX 45 AE9 SER D 557 ALA D 565 1 9 HELIX 46 AF1 GLU D 569 ILE D 588 1 20 HELIX 47 AF2 ILE D 588 VAL D 595 1 8 HELIX 48 AF3 LEU D 630 LYS D 635 1 6 HELIX 49 AF4 ILE D 636 GLN D 638 5 3 HELIX 50 AF5 GLN D 656 GLU D 667 1 12 HELIX 51 AF6 ASP D 668 ARG D 677 1 10 HELIX 52 AF7 ASP D 680 GLN D 691 1 12 HELIX 53 AF8 SER D 693 VAL D 697 5 5 HELIX 54 AF9 THR D 698 TYR D 714 1 17 HELIX 55 AG1 SER D 717 ASN D 726 1 10 HELIX 56 AG2 SER D 728 PHE D 743 1 16 HELIX 57 AG3 PHE D 743 GLY D 761 1 19 HELIX 58 AG4 PRO D 774 SER D 778 5 5 HELIX 59 AG5 ASN D 780 GLU D 818 1 39 HELIX 60 AG6 GLU D 840 ALA D 855 1 16 SHEET 1 AA1 6 THR A 302 LEU A 303 0 SHEET 2 AA1 6 GLY A 342 LEU A 346 1 O ARG A 343 N THR A 302 SHEET 3 AA1 6 GLY A 334 ASN A 339 -1 N VAL A 337 O PHE A 344 SHEET 4 AA1 6 LYS A 315 GLU A 321 -1 N ALA A 317 O VAL A 338 SHEET 5 AA1 6 LYS A 367 MET A 370 1 O SER A 369 N ALA A 316 SHEET 6 AA1 6 VAL A 390 ASP A 393 1 O PHE A 392 N MET A 370 SHEET 1 AA2 3 LYS A 601 VAL A 602 0 SHEET 2 AA2 3 VAL A 493 VAL A 495 -1 N VAL A 493 O VAL A 602 SHEET 3 AA2 3 PHE A 640 VAL A 641 -1 O VAL A 641 N LYS A 494 SHEET 1 AA3 2 ILE A 605 ASN A 607 0 SHEET 2 AA3 2 SER A 617 THR A 619 -1 O THR A 619 N ILE A 605 SHEET 1 AA4 4 HIS A 823 GLN A 827 0 SHEET 2 AA4 4 GLU A 831 PRO A 837 -1 O ILE A 833 N LEU A 825 SHEET 3 AA4 4 TRP A 647 TYR A 654 -1 N PHE A 650 O LEU A 834 SHEET 4 AA4 4 VAL A 864 GLY A 869 -1 O HIS A 867 N ALA A 651 SHEET 1 AA5 2 TYR A 762 THR A 764 0 SHEET 2 AA5 2 ARG A 770 TYR A 772 -1 O ARG A 771 N VAL A 763 SHEET 1 AA6 6 THR D 302 ALA D 304 0 SHEET 2 AA6 6 GLY D 342 LEU D 346 1 O ARG D 343 N THR D 302 SHEET 3 AA6 6 GLY D 334 ASN D 339 -1 N VAL D 337 O PHE D 344 SHEET 4 AA6 6 LYS D 315 GLU D 321 -1 N ALA D 317 O VAL D 338 SHEET 5 AA6 6 LYS D 367 MET D 370 1 O SER D 369 N LEU D 318 SHEET 6 AA6 6 VAL D 390 ASP D 393 1 O PHE D 392 N MET D 370 SHEET 1 AA7 3 LYS D 601 VAL D 602 0 SHEET 2 AA7 3 VAL D 493 VAL D 495 -1 N VAL D 493 O VAL D 602 SHEET 3 AA7 3 PHE D 640 VAL D 641 -1 O VAL D 641 N LYS D 494 SHEET 1 AA8 2 ILE D 605 ASN D 607 0 SHEET 2 AA8 2 SER D 617 THR D 619 -1 O THR D 619 N ILE D 605 SHEET 1 AA9 4 HIS D 823 GLN D 827 0 SHEET 2 AA9 4 GLU D 831 PRO D 837 -1 O ILE D 833 N LEU D 825 SHEET 3 AA9 4 TRP D 647 TYR D 654 -1 N PHE D 650 O LEU D 834 SHEET 4 AA9 4 VAL D 864 GLY D 869 -1 O HIS D 867 N ALA D 651 SHEET 1 AB1 2 TYR D 762 THR D 764 0 SHEET 2 AB1 2 ARG D 770 TYR D 772 -1 O ARG D 771 N VAL D 763 LINK O3' DG B 8 P BC42 B 9 1555 1555 1.60 LINK O3' DG B 8 P AC42 B 9 1555 1555 1.60 LINK N AC42 B 9 P A DG B 10 1555 1555 1.64 LINK O3' DG E 8 P AC42 E 9 1555 1555 1.60 LINK O3' DG E 8 P BC42 E 9 1555 1555 1.60 LINK N AC42 E 9 P A DG E 10 1555 1555 1.64 LINK OD2 ASP A 653 CA CA A 903 1555 1555 2.79 LINK O TYR A 654 CA CA A 903 1555 1555 2.63 LINK OD2 ASP A 830 CA CA A 903 1555 1555 2.73 LINK O2 ADPO A 901 CA CA A 903 1555 1555 2.84 LINK O6 ADPO A 901 CA CA A 903 1555 1555 3.10 LINK O2GBDGT A 902 CA CA A 903 1555 1555 2.91 LINK O2BBDGT A 902 CA CA A 903 1555 1555 3.17 LINK O2ABDGT A 902 CA CA A 903 1555 1555 2.54 LINK CA CA A 903 O HOH A1051 1555 1555 3.02 LINK CA CA A 903 OP2A DG B 10 1555 1555 2.31 LINK OD2 ASP D 653 CA CA D 903 1555 1555 2.91 LINK O TYR D 654 CA CA D 903 1555 1555 2.51 LINK OD2 ASP D 830 CA CA D 903 1555 1555 2.51 LINK O2 ADPO D 901 CA CA D 903 1555 1555 2.65 LINK O6 ADPO D 901 CA CA D 903 1555 1555 2.97 LINK O2GBDGT D 902 CA CA D 903 1555 1555 2.70 LINK O2BBDGT D 902 CA CA D 903 1555 1555 2.88 LINK O2ABDGT D 902 CA CA D 903 1555 1555 2.65 LINK CA CA D 903 O HOH D1003 1555 1555 3.09 LINK CA CA D 903 OP2A DG E 10 1555 1555 2.23 CISPEP 1 GLU A 620 PRO A 621 0 -1.05 CISPEP 2 GLU D 620 PRO D 621 0 2.65 CRYST1 93.500 108.932 149.356 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 0.010695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006695 0.00000