HEADER TRANSFERASE, LYASE/DNA 13-MAY-12 4F5N TITLE OPEN TERNARY COMPLEX OF R283K DNA POLYMERASE BETA WITH A METAL FREE TITLE 2 DCTP ANALOG COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA POLYMERASE BETA; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.7, 4.2.99.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 9 3'); COMPND 10 CHAIN: T; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'); COMPND 14 CHAIN: P; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 18 CHAIN: D; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: POLB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PWL11; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: POLYDEOXYRIBONUCLEOTIDE FROM IDT; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 OTHER_DETAILS: POLYDEOXYRIBONUCLEOTIDE FROM IDT; SOURCE 21 MOL_ID: 4; SOURCE 22 SYNTHETIC: YES; SOURCE 23 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 24 ORGANISM_TAXID: 32630; SOURCE 25 OTHER_DETAILS: POLYDEOXYRIBONUCLEOTIDE FROM IDT KEYWDS TRANSFERASE, LYASE/DNA, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,W.A.BEARD,S.H.WILSON REVDAT 3 13-SEP-23 4F5N 1 REMARK SEQADV LINK REVDAT 2 17-JUL-19 4F5N 1 REMARK REVDAT 1 12-DEC-12 4F5N 0 JRNL AUTH B.D.FREUDENTHAL,W.A.BEARD,S.H.WILSON JRNL TITL STRUCTURES OF DNTP INTERMEDIATE STATES DURING DNA POLYMERASE JRNL TITL 2 ACTIVE SITE ASSEMBLY. JRNL REF STRUCTURE V. 20 1829 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22959623 JRNL DOI 10.1016/J.STR.2012.08.008 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 22.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 39766 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4016 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 22.1000 - 5.4970 1.00 1338 137 0.1839 0.1968 REMARK 3 2 5.4970 - 4.3742 1.00 1300 152 0.1619 0.1676 REMARK 3 3 4.3742 - 3.8245 1.00 1302 139 0.1520 0.1774 REMARK 3 4 3.8245 - 3.4763 1.00 1305 133 0.1659 0.1871 REMARK 3 5 3.4763 - 3.2280 1.00 1303 144 0.1746 0.1825 REMARK 3 6 3.2280 - 3.0381 1.00 1272 155 0.1917 0.2194 REMARK 3 7 3.0381 - 2.8863 0.99 1265 163 0.2021 0.2248 REMARK 3 8 2.8863 - 2.7609 0.98 1277 146 0.1915 0.2300 REMARK 3 9 2.7609 - 2.6548 0.99 1262 145 0.2005 0.2493 REMARK 3 10 2.6548 - 2.5634 0.98 1269 146 0.2016 0.2299 REMARK 3 11 2.5634 - 2.4833 0.98 1252 145 0.2090 0.2479 REMARK 3 12 2.4833 - 2.4124 0.98 1289 123 0.2006 0.2730 REMARK 3 13 2.4124 - 2.3490 0.98 1266 124 0.1998 0.2348 REMARK 3 14 2.3490 - 2.2917 0.98 1261 154 0.1963 0.2369 REMARK 3 15 2.2917 - 2.2397 0.99 1267 151 0.1906 0.2361 REMARK 3 16 2.2397 - 2.1921 0.98 1259 138 0.1957 0.2524 REMARK 3 17 2.1921 - 2.1483 0.98 1282 140 0.2021 0.2553 REMARK 3 18 2.1483 - 2.1078 0.98 1254 142 0.2039 0.2783 REMARK 3 19 2.1078 - 2.0701 0.99 1256 143 0.1950 0.2339 REMARK 3 20 2.0701 - 2.0351 0.98 1266 131 0.1923 0.2494 REMARK 3 21 2.0351 - 2.0023 0.97 1232 142 0.1935 0.2374 REMARK 3 22 2.0023 - 1.9715 0.95 1238 140 0.2007 0.2779 REMARK 3 23 1.9715 - 1.9425 0.94 1185 140 0.2208 0.3050 REMARK 3 24 1.9425 - 1.9152 0.92 1212 142 0.2175 0.2930 REMARK 3 25 1.9152 - 1.8893 0.91 1115 122 0.2210 0.2178 REMARK 3 26 1.8893 - 1.8648 0.88 1154 135 0.2277 0.2890 REMARK 3 27 1.8648 - 1.8415 0.85 1067 120 0.2323 0.2950 REMARK 3 28 1.8415 - 1.8193 0.79 1028 117 0.2454 0.3267 REMARK 3 29 1.8193 - 1.7981 0.74 974 107 0.2572 0.3263 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 : 0.35 REMARK 3 B_SOL : 43.78 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.64100 REMARK 3 B22 (A**2) : 0.73800 REMARK 3 B33 (A**2) : -3.37900 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.23360 REMARK 3 B23 (A**2) : 0.00000 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 3371 REMARK 3 ANGLE : 1.027 4674 REMARK 3 CHIRALITY : 0.057 513 REMARK 3 PLANARITY : 0.003 486 REMARK 3 DIHEDRAL : 19.131 1312 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 4F5N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : MIRRORS VARIMAXHF REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 209537 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.04700 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.22900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 3ISB.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM IMIDAZOLE, 350MM SODIUM ACETATE, REMARK 280 18% PEG3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 39.59050 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER IN EACH ASYMMETRIC REMARK 300 UNIT. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, T, P, 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 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LYS A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 ALA A 6 REMARK 465 PRO A 7 REMARK 465 THR A 205 REMARK 465 LYS A 206 REMARK 465 GLN A 207 REMARK 465 LYS A 244 REMARK 465 ASN A 245 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 GLU A 203 CG CD OE1 OE2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 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 680 O HOH P 122 2.07 REMARK 500 O1G 6CF A 404 O HOH A 879 2.08 REMARK 500 OP2 DG D 5 O HOH D 106 2.10 REMARK 500 O HOH A 742 O HOH A 873 2.10 REMARK 500 O HOH A 826 O HOH A 851 2.12 REMARK 500 O HOH A 862 O HOH A 879 2.15 REMARK 500 O1B 6CF A 404 O HOH A 879 2.16 REMARK 500 O HOH A 884 O HOH A 906 2.17 REMARK 500 OD1 ASP A 190 O HOH A 864 2.18 REMARK 500 OP2 DC T 16 O HOH T 115 2.19 REMARK 500 O HOH A 686 O HOH A 718 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 DG D 1 P DG 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 T 2 O4' - C1' - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 DC T 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG T 7 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DG T 7 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DA T 14 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT D 2 O4' - C1' - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT D 2 N3 - C4 - O4 ANGL. DEV. = 3.6 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 170 117.11 -160.63 REMARK 500 CYS A 178 -156.52 -112.12 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 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 91.5 REMARK 620 3 VAL A 65 O 89.0 98.8 REMARK 620 4 HOH A 570 O 87.4 86.0 174.2 REMARK 620 5 DC D 3 OP1 168.8 98.9 93.5 89.1 REMARK 620 6 HOH D 102 O 86.4 173.2 87.7 87.5 82.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 HOH A 502 O 82.0 REMARK 620 3 HOH A 517 O 82.2 161.9 REMARK 620 4 HOH A 819 O 114.5 94.8 83.8 REMARK 620 5 HOH P 101 O 75.4 84.2 100.2 169.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 94.4 REMARK 620 3 ILE A 106 O 97.9 89.5 REMARK 620 4 HOH A 502 O 83.0 95.1 175.3 REMARK 620 5 DG P 9 OP1 162.0 97.8 95.4 82.8 REMARK 620 6 HOH P 101 O 82.5 176.0 88.5 87.0 85.8 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 NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 6CF A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F5R RELATED DB: PDB REMARK 900 RELATED ID: 4F5Q RELATED DB: PDB REMARK 900 RELATED ID: 4F5P RELATED DB: PDB REMARK 900 RELATED ID: 4F5O RELATED DB: PDB DBREF 4F5N A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4F5N T 1 16 PDB 4F5N 4F5N 1 16 DBREF 4F5N P 1 10 PDB 4F5N 4F5N 1 10 DBREF 4F5N D 1 5 PDB 4F5N 4F5N 1 5 SEQADV 4F5N LYS A 283 UNP P06746 ARG 283 ENGINEERED MUTATION SEQRES 1 A 335 MET SER LYS ARG LYS ALA PRO GLN GLU THR LEU ASN GLY SEQRES 2 A 335 GLY ILE THR ASP MET LEU THR GLU LEU ALA ASN PHE GLU SEQRES 3 A 335 LYS ASN VAL SER GLN ALA ILE HIS LYS TYR ASN ALA TYR SEQRES 4 A 335 ARG LYS ALA ALA SER VAL ILE ALA LYS TYR PRO HIS LYS SEQRES 5 A 335 ILE LYS SER GLY ALA GLU ALA LYS LYS LEU PRO GLY VAL SEQRES 6 A 335 GLY THR LYS ILE ALA GLU LYS ILE ASP GLU PHE LEU ALA SEQRES 7 A 335 THR GLY LYS LEU ARG LYS LEU GLU LYS ILE ARG GLN ASP SEQRES 8 A 335 ASP THR SER SER SER ILE ASN PHE LEU THR ARG VAL SER SEQRES 9 A 335 GLY ILE GLY PRO SER ALA ALA ARG LYS PHE VAL ASP GLU SEQRES 10 A 335 GLY ILE LYS THR LEU GLU ASP LEU ARG LYS ASN GLU ASP SEQRES 11 A 335 LYS LEU ASN HIS HIS GLN ARG ILE GLY LEU LYS TYR PHE SEQRES 12 A 335 GLY ASP PHE GLU LYS ARG ILE PRO ARG GLU GLU MET LEU SEQRES 13 A 335 GLN MET GLN ASP ILE VAL LEU ASN GLU VAL LYS LYS VAL SEQRES 14 A 335 ASP SER GLU TYR ILE ALA THR VAL CYS GLY SER PHE ARG SEQRES 15 A 335 ARG GLY ALA GLU SER SER GLY ASP MET ASP VAL LEU LEU SEQRES 16 A 335 THR HIS PRO SER PHE THR SER GLU SER THR LYS GLN PRO SEQRES 17 A 335 LYS LEU LEU HIS GLN VAL VAL GLU GLN LEU GLN LYS VAL SEQRES 18 A 335 HIS PHE ILE THR ASP THR LEU SER LYS GLY GLU THR LYS SEQRES 19 A 335 PHE MET GLY VAL CYS GLN LEU PRO SER LYS ASN ASP GLU SEQRES 20 A 335 LYS GLU TYR PRO HIS ARG ARG ILE ASP ILE ARG LEU ILE SEQRES 21 A 335 PRO LYS ASP GLN TYR TYR CYS GLY VAL LEU TYR PHE THR SEQRES 22 A 335 GLY SER ASP ILE PHE ASN LYS ASN MET LYS ALA HIS ALA SEQRES 23 A 335 LEU GLU LYS GLY PHE THR ILE ASN GLU TYR THR ILE ARG SEQRES 24 A 335 PRO LEU GLY VAL THR GLY VAL ALA GLY GLU PRO LEU PRO SEQRES 25 A 335 VAL ASP SER GLU LYS ASP ILE PHE ASP TYR ILE GLN TRP SEQRES 26 A 335 LYS TYR ARG GLU PRO LYS ASP ARG SER GLU SEQRES 1 T 16 DC DC DG DA DC DG DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 10 DG DC DT DG DA DT DG DC DG DC SEQRES 1 D 5 DG DT DC DG DG HET NA A 401 1 HET NA A 402 1 HET NA A 403 1 HET 6CF A 404 30 HETNAM NA SODIUM ION HETNAM 6CF 2'-DEOXY-5'-O-[(S)-{DIFLUORO[(S)-HYDROXY(PHOSPHONOOXY) HETNAM 2 6CF PHOSPHORYL]METHYL}(HYDROXY)PHOSPHORYL]CYTIDINE FORMUL 5 NA 3(NA 1+) FORMUL 8 6CF C10 H16 F2 N3 O12 P3 FORMUL 9 HOH *563(H2 O) HELIX 1 1 GLN A 8 VAL A 29 1 22 HELIX 2 2 ALA A 32 LYS A 48 1 17 HELIX 3 3 SER A 55 LYS A 61 1 7 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 GLN A 90 1 9 HELIX 6 6 ASP A 91 THR A 101 1 11 HELIX 7 7 GLY A 107 GLU A 117 1 11 HELIX 8 8 THR A 121 LYS A 127 1 7 HELIX 9 9 ASN A 128 LEU A 132 5 5 HELIX 10 10 ASN A 133 TYR A 142 1 10 HELIX 11 11 TYR A 142 LYS A 148 1 7 HELIX 12 12 ARG A 152 ASP A 170 1 19 HELIX 13 13 GLY A 179 ARG A 182 5 4 HELIX 14 14 LYS A 209 VAL A 221 1 13 HELIX 15 15 PRO A 261 ASP A 263 5 3 HELIX 16 16 GLN A 264 GLY A 274 1 11 HELIX 17 17 SER A 275 LYS A 289 1 15 HELIX 18 18 SER A 315 ILE A 323 1 9 HELIX 19 19 GLU A 329 ARG A 333 5 5 SHEET 1 A 2 ILE A 150 PRO A 151 0 SHEET 2 A 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 B 5 ILE A 174 CYS A 178 0 SHEET 2 B 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 B 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N CYS A 239 O ARG A 253 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N SER A 229 O MET A 236 SHEET 1 C 2 PHE A 291 ILE A 293 0 SHEET 2 C 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O LYS A 60 NA NA A 403 1555 1555 2.42 LINK O LEU A 62 NA NA A 403 1555 1555 2.35 LINK O VAL A 65 NA NA A 403 1555 1555 2.31 LINK O THR A 101 NA NA A 401 1555 1555 2.52 LINK O THR A 101 NA NA A 402 1555 1555 2.36 LINK O VAL A 103 NA NA A 402 1555 1555 2.38 LINK O ILE A 106 NA NA A 402 1555 1555 2.34 LINK NA NA A 401 O HOH A 502 1555 1555 2.68 LINK NA NA A 401 O HOH A 517 1555 1555 2.60 LINK NA NA A 401 O HOH A 819 1555 1555 2.94 LINK NA NA A 401 O HOH P 101 1555 1555 2.90 LINK NA NA A 402 O HOH A 502 1555 1555 2.77 LINK NA NA A 402 OP1 DG P 9 1555 1555 2.39 LINK NA NA A 402 O HOH P 101 1555 1555 2.68 LINK NA NA A 403 O HOH A 570 1555 1555 2.62 LINK NA NA A 403 OP1 DC D 3 1555 1555 2.71 LINK NA NA A 403 O HOH D 102 1555 1555 2.60 CISPEP 1 GLY A 274 SER A 275 0 2.25 SITE 1 AC1 6 THR A 101 NA A 402 HOH A 502 HOH A 517 SITE 2 AC1 6 HOH A 819 HOH P 101 SITE 1 AC2 7 THR A 101 VAL A 103 ILE A 106 NA A 401 SITE 2 AC2 7 HOH A 502 DG P 9 HOH P 101 SITE 1 AC3 6 LYS A 60 LEU A 62 VAL A 65 HOH A 570 SITE 2 AC3 6 DC D 3 HOH D 102 SITE 1 AC4 20 ARG A 149 SER A 180 ARG A 183 GLY A 189 SITE 2 AC4 20 TYR A 271 GLY A 274 SER A 275 ASP A 276 SITE 3 AC4 20 ASN A 279 HOH A 541 HOH A 601 HOH A 652 SITE 4 AC4 20 HOH A 713 HOH A 793 HOH A 818 HOH A 862 SITE 5 AC4 20 HOH A 869 HOH A 879 DC P 10 DG T 6 CRYST1 54.322 79.181 54.857 90.00 105.53 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.018409 0.000000 0.005116 0.00000 SCALE2 0.000000 0.012629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018920 0.00000 CONECT 406 3216 CONECT 424 3216 CONECT 443 3216 CONECT 728 3214 3215 CONECT 746 3215 CONECT 763 3215 CONECT 3066 3215 CONECT 3151 3216 CONECT 3214 728 3248 3263 3565 CONECT 3214 3725 CONECT 3215 728 746 763 3066 CONECT 3215 3248 3725 CONECT 3216 406 424 443 3151 CONECT 3216 3316 3782 CONECT 3217 3219 3227 3228 CONECT 3218 3230 3235 3240 3246 CONECT 3219 3217 3220 3222 CONECT 3220 3219 CONECT 3221 3231 3236 3240 3241 CONECT 3222 3219 3224 CONECT 3223 3232 3237 3241 3242 CONECT 3224 3222 3225 3226 CONECT 3225 3224 CONECT 3226 3224 3227 CONECT 3227 3217 3226 CONECT 3228 3217 3233 3244 CONECT 3229 3240 CONECT 3230 3218 CONECT 3231 3221 CONECT 3232 3223 CONECT 3233 3228 3238 CONECT 3234 3240 CONECT 3235 3218 CONECT 3236 3221 CONECT 3237 3223 CONECT 3238 3233 3239 3243 CONECT 3239 3238 CONECT 3240 3218 3221 3229 3234 CONECT 3241 3221 3223 CONECT 3242 3223 CONECT 3243 3238 3244 3245 CONECT 3244 3228 3243 CONECT 3245 3243 3246 CONECT 3246 3218 3245 CONECT 3248 3214 3215 CONECT 3263 3214 CONECT 3316 3216 CONECT 3565 3214 CONECT 3725 3214 3215 CONECT 3782 3216 MASTER 385 0 4 19 9 0 11 6 3805 4 50 30 END