PDB Short entry for 4KLD HEADER TRANSFERASE, LYASE/DNA 07-MAY-13 4KLD TITLE DNA POLYMERASE BETA MATCHED SUBSTRATE COMPLEX WITH CA2+, 0 S COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'; COMPND 3 CHAIN: T; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'; COMPND 7 CHAIN: P; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: DNA POLYMERASE BETA; COMPND 15 CHAIN: A; COMPND 16 EC: 2.7.7.7, 4.2.99.-; COMPND 17 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: POLB; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: TAP56; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PWL11 KEYWDS DNA POLYMERASE, TRANSFERASE, LYASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.D.FREUDENTHAL,W.A.BEARD,D.D.SHOCK,S.H.WILSON REVDAT 3 20-SEP-23 4KLD 1 REMARK LINK REVDAT 2 15-NOV-17 4KLD 1 REMARK REVDAT 1 17-JUL-13 4KLD 0 JRNL AUTH B.D.FREUDENTHAL,W.A.BEARD,D.D.SHOCK,S.H.WILSON JRNL TITL OBSERVING A DNA POLYMERASE CHOOSE RIGHT FROM WRONG. JRNL REF CELL(CAMBRIDGE,MASS.) V. 154 157 2013 JRNL REFN ISSN 0092-8674 JRNL PMID 23827680 JRNL DOI 10.1016/J.CELL.2013.05.048 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.15 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.2 REMARK 3 NUMBER OF REFLECTIONS : 28482 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2848 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 23.1488 - 5.1818 1.00 1518 161 0.1849 0.1884 REMARK 3 2 5.1818 - 4.1205 0.91 1351 143 0.1574 0.2187 REMARK 3 3 4.1205 - 3.6019 0.92 1367 140 0.1665 0.2236 REMARK 3 4 3.6019 - 3.2736 0.99 1476 145 0.1879 0.2361 REMARK 3 5 3.2736 - 3.0395 0.99 1444 173 0.2018 0.2585 REMARK 3 6 3.0395 - 2.8606 0.98 1438 162 0.2126 0.2663 REMARK 3 7 2.8606 - 2.7176 0.97 1424 157 0.2241 0.2910 REMARK 3 8 2.7176 - 2.5994 0.96 1422 150 0.2348 0.2581 REMARK 3 9 2.5994 - 2.4995 0.95 1383 150 0.2286 0.3095 REMARK 3 10 2.4995 - 2.4133 0.95 1383 158 0.2268 0.3350 REMARK 3 11 2.4133 - 2.3380 0.97 1419 176 0.2130 0.2663 REMARK 3 12 2.3380 - 2.2712 0.92 1339 147 0.2089 0.2704 REMARK 3 13 2.2712 - 2.2114 0.95 1366 169 0.2110 0.2703 REMARK 3 14 2.2114 - 2.1575 0.92 1374 146 0.2111 0.2747 REMARK 3 15 2.1575 - 2.1085 0.89 1299 152 0.2145 0.3224 REMARK 3 16 2.1085 - 2.0637 0.88 1260 163 0.2244 0.2898 REMARK 3 17 2.0637 - 2.0224 0.82 1210 129 0.2423 0.3167 REMARK 3 18 2.0224 - 1.9843 0.80 1174 120 0.2461 0.2917 REMARK 3 19 1.9843 - 1.9489 0.52 771 80 0.2421 0.3566 REMARK 3 20 1.9489 - 1.9160 0.15 216 27 0.2603 0.3028 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 60.96 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.40480 REMARK 3 B22 (A**2) : -0.59560 REMARK 3 B33 (A**2) : -3.80930 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.54540 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 : 0.011 3473 REMARK 3 ANGLE : 1.237 4829 REMARK 3 CHIRALITY : 0.072 522 REMARK 3 PLANARITY : 0.004 508 REMARK 3 DIHEDRAL : 19.291 1344 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 4KLD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079483. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-AUG-12 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 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 92 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30191 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.916 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3C2M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 CHLORIDE, 17% PEG3350, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 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 40.20000 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 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: 6230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -123.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: T, P, D, 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 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 GLN A 8 REMARK 465 GLU A 9 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 A 248 CG CD CE NZ REMARK 470 VAL A 303 CG1 CG2 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 DA P 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT D 2 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.9 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 LYS A 120 26.90 -154.51 REMARK 500 CYS A 178 -151.11 -115.96 REMARK 500 SER A 275 -179.77 -69.84 REMARK 500 ASN A 294 -165.63 -124.33 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 404 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 111 O 96.4 REMARK 620 3 THR A 101 O 174.7 79.9 REMARK 620 4 VAL A 103 O 90.8 166.1 93.6 REMARK 620 5 ILE A 106 O 94.0 80.1 89.2 87.6 REMARK 620 6 HOH A 531 O 93.8 109.1 83.8 82.1 167.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC P 10 O3' REMARK 620 2 ASP A 190 OD2 149.9 REMARK 620 3 ASP A 190 OD1 157.1 51.0 REMARK 620 4 ASP A 192 OD1 81.6 123.5 87.5 REMARK 620 5 ASP A 256 OD2 73.4 88.2 127.3 91.5 REMARK 620 6 DCP A 401 O2A 88.2 109.1 70.6 84.2 161.6 REMARK 620 7 HOH A 528 O 80.6 80.3 101.5 153.1 102.4 75.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC D 3 OP1 REMARK 620 2 HOH D 101 O 94.5 REMARK 620 3 LYS A 60 O 176.8 84.1 REMARK 620 4 LEU A 62 O 92.8 172.6 88.6 REMARK 620 5 VAL A 65 O 90.3 84.5 86.8 94.1 REMARK 620 6 HOH A 567 O 89.2 102.6 93.9 78.8 172.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 190 O 68.0 REMARK 620 3 ASP A 192 OD2 95.8 88.8 REMARK 620 4 DCP A 401 O3G 97.5 97.8 166.6 REMARK 620 5 DCP A 401 O2A 81.5 148.9 88.3 91.9 REMARK 620 6 DCP A 401 O2B 158.9 132.7 89.5 77.4 78.3 REMARK 620 7 HOH A 529 O 124.9 56.9 85.9 88.0 153.4 75.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KLE RELATED DB: PDB REMARK 900 RELATED ID: 4KLF RELATED DB: PDB REMARK 900 RELATED ID: 4KLG RELATED DB: PDB REMARK 900 RELATED ID: 4KLH RELATED DB: PDB REMARK 900 RELATED ID: 4KLI RELATED DB: PDB REMARK 900 RELATED ID: 4KLJ RELATED DB: PDB REMARK 900 RELATED ID: 4KLL RELATED DB: PDB REMARK 900 RELATED ID: 4KLM RELATED DB: PDB REMARK 900 RELATED ID: 4KLO RELATED DB: PDB REMARK 900 RELATED ID: 4KLP RELATED DB: PDB REMARK 900 RELATED ID: 4KLQ RELATED DB: PDB REMARK 900 RELATED ID: 4KLS RELATED DB: PDB REMARK 900 RELATED ID: 4KLT RELATED DB: PDB REMARK 900 RELATED ID: 4KLU RELATED DB: PDB DBREF 4KLD A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 4KLD T 1 16 PDB 4KLD 4KLD 1 16 DBREF 4KLD P 1 10 PDB 4KLD 4KLD 1 10 DBREF 4KLD D 1 5 PDB 4KLD 4KLD 1 5 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 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 ARG 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 HET DCP A 401 28 HET CA A 402 1 HET CA A 403 1 HET NA A 404 1 HET NA A 405 1 HET CL A 406 1 HET CL A 407 1 HET CL A 408 1 HET CL A 409 1 HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 5 DCP C9 H16 N3 O13 P3 FORMUL 6 CA 2(CA 2+) FORMUL 8 NA 2(NA 1+) FORMUL 10 CL 4(CL 1-) FORMUL 14 HOH *197(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 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 ASP A 91 1 10 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 LYS A 209 VAL A 221 1 13 HELIX 14 14 PRO A 261 ASP A 263 5 3 HELIX 15 15 GLN A 264 GLY A 274 1 11 HELIX 16 16 SER A 275 LYS A 289 1 15 HELIX 17 17 SER A 315 ILE A 323 1 9 HELIX 18 18 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 VAL A 177 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 ASP A 256 N VAL A 193 SHEET 4 B 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 SHEET 5 B 5 ILE A 224 LYS A 230 -1 N LEU A 228 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 OP1 DG P 9 NA NA A 404 1555 1555 2.41 LINK O3' DC P 10 CA CA A 403 1555 1555 2.64 LINK O HOH P 111 NA NA A 404 1555 1555 2.66 LINK OP1 DC D 3 NA NA A 405 1555 1555 2.59 LINK O HOH D 101 NA NA A 405 1555 1555 2.28 LINK O LYS A 60 NA NA A 405 1555 1555 2.41 LINK O LEU A 62 NA NA A 405 1555 1555 2.66 LINK O VAL A 65 NA NA A 405 1555 1555 2.37 LINK O THR A 101 NA NA A 404 1555 1555 2.30 LINK O VAL A 103 NA NA A 404 1555 1555 2.59 LINK O ILE A 106 NA NA A 404 1555 1555 2.54 LINK OD1 ASP A 190 CA CA A 402 1555 1555 2.26 LINK O ASP A 190 CA CA A 402 1555 1555 3.06 LINK OD2 ASP A 190 CA CA A 403 1555 1555 2.48 LINK OD1 ASP A 190 CA CA A 403 1555 1555 2.59 LINK OD2 ASP A 192 CA CA A 402 1555 1555 2.40 LINK OD1 ASP A 192 CA CA A 403 1555 1555 2.39 LINK OD2 ASP A 256 CA CA A 403 1555 1555 2.39 LINK O3G DCP A 401 CA CA A 402 1555 1555 2.19 LINK O2A DCP A 401 CA CA A 402 1555 1555 2.28 LINK O2B DCP A 401 CA CA A 402 1555 1555 2.47 LINK O2A DCP A 401 CA CA A 403 1555 1555 2.54 LINK CA CA A 402 O HOH A 529 1555 1555 2.67 LINK CA CA A 403 O HOH A 528 1555 1555 2.65 LINK NA NA A 404 O HOH A 531 1555 1555 2.44 LINK NA NA A 405 O HOH A 567 1555 1555 2.55 CISPEP 1 GLY A 274 SER A 275 0 0.56 SITE 1 AC1 19 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AC1 19 GLY A 189 ASP A 190 ASP A 192 TYR A 271 SITE 3 AC1 19 PHE A 272 THR A 273 GLY A 274 ASP A 276 SITE 4 AC1 19 ASN A 279 CA A 402 CA A 403 HOH A 516 SITE 5 AC1 19 HOH A 528 DC P 10 DG T 6 SITE 1 AC2 5 ASP A 190 ASP A 192 DCP A 401 CA A 403 SITE 2 AC2 5 HOH A 529 SITE 1 AC3 7 ASP A 190 ASP A 192 ASP A 256 DCP A 401 SITE 2 AC3 7 CA A 402 HOH A 528 DC P 10 SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 HOH A 531 SITE 2 AC4 6 DG P 9 HOH P 111 SITE 1 AC5 6 LYS A 60 LEU A 62 VAL A 65 HOH A 567 SITE 2 AC5 6 DC D 3 HOH D 101 SITE 1 AC6 4 GLN A 264 TYR A 266 CYS A 267 VAL A 313 SITE 1 AC7 3 ALA A 32 HIS A 34 LYS A 35 SITE 1 AC8 2 LEU A 82 ARG A 89 SITE 1 AC9 4 ASN A 294 THR A 297 ARG A 299 HOH A 625 CRYST1 50.800 80.400 55.500 90.00 107.90 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 0.019685 0.000000 0.006358 0.00000 SCALE2 0.000000 0.012438 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018935 0.00000