PDB Short entry for 3RH5 HEADER TRANSFERASE/DNA 11-APR-11 3RH5 TITLE DNA POLYMERASE BETA MUTANT (Y271) WITH A DIDEOXY-TERMINATED PRIMER TITLE 2 WITH AN INCOMING DEOXYNUCLEOTIDE (DCTP) 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: 5'-D(*CP*CP*GP*AP*CP*GP*CP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'; COMPND 9 CHAIN: T; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DDG))-3'; COMPND 13 CHAIN: P; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: 5'-D(P*GP*TP*CP*GP*G)-3'; COMPND 17 CHAIN: D; COMPND 18 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: PWL11; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 MOL_ID: 3; SOURCE 13 SYNTHETIC: YES; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES KEYWDS DNA POLYMERASE BETA MUTANT, NUCLEOTIDE TRANSFERASE, RIBONUCLEOTIDE KEYWDS 2 INSERTION, DCTP, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR N.A.CAVANAUGH,W.A.BEARD,V.K.BATRA,L.PERERA,L.G.PEDERSEN,S.H.WILSON REVDAT 4 13-SEP-23 3RH5 1 REMARK SEQADV LINK REVDAT 3 21-SEP-11 3RH5 1 JRNL REVDAT 2 20-JUL-11 3RH5 1 JRNL REVDAT 1 06-JUL-11 3RH5 0 JRNL AUTH N.A.CAVANAUGH,W.A.BEARD,V.K.BATRA,L.PERERA,L.G.PEDERSEN, JRNL AUTH 2 S.H.WILSON JRNL TITL MOLECULAR INSIGHTS INTO DNA POLYMERASE DETERRENTS FOR JRNL TITL 2 RIBONUCLEOTIDE INSERTION. JRNL REF J.BIOL.CHEM. V. 286 31650 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21733843 JRNL DOI 10.1074/JBC.M111.253401 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 82.1 REMARK 3 NUMBER OF REFLECTIONS : 20393 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.730 REMARK 3 FREE R VALUE TEST SET COUNT : 1985 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 20.7059 - 4.5021 0.96 2217 223 0.1676 0.2266 REMARK 3 2 4.5021 - 3.5795 0.96 2177 236 0.1557 0.2206 REMARK 3 3 3.5795 - 3.1288 0.99 2214 236 0.1647 0.2245 REMARK 3 4 3.1288 - 2.8435 0.69 1540 160 0.2271 0.3277 REMARK 3 5 2.8435 - 2.6401 0.64 1429 164 0.2280 0.2989 REMARK 3 6 2.6401 - 2.4847 0.68 1522 154 0.2138 0.3167 REMARK 3 7 2.4847 - 2.3605 0.73 1620 190 0.2306 0.3145 REMARK 3 8 2.3605 - 2.2579 0.79 1727 232 0.2409 0.3642 REMARK 3 9 2.2579 - 2.1710 0.87 1976 195 0.2399 0.3254 REMARK 3 10 2.1710 - 2.0962 0.89 1986 195 0.2313 0.3269 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 : 0.38 REMARK 3 B_SOL : 42.96 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.460 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.56660 REMARK 3 B22 (A**2) : -3.91680 REMARK 3 B33 (A**2) : -2.64980 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 4.61850 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 : 0.007 3417 REMARK 3 ANGLE : 1.202 4741 REMARK 3 CHIRALITY : 0.063 520 REMARK 3 PLANARITY : 0.005 496 REMARK 3 DIHEDRAL : 22.223 1372 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 3RH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-APR-11. REMARK 100 THE DEPOSITION ID IS D_1000064925. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VIRAMAX 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 : 24357 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.096 REMARK 200 RESOLUTION RANGE LOW (A) : 20.705 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG3350, 350 MM SODIUM ACETATE, 50 REMARK 280 MM IMIDAZOLE, PH 7.0, 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 39.96000 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: 7960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -131.0 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 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 VAL A 303 CG1 CG2 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 -0.131 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 DG T 6 O4' - C1' - N9 ANGL. DEV. = -6.9 DEGREES REMARK 500 DA T 11 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT P 6 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC P 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DT D 2 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG D 5 O4' - C1' - N9 ANGL. DEV. = 2.5 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 PRO A 50 34.50 -95.28 REMARK 500 LYS A 120 16.98 -158.04 REMARK 500 CYS A 178 -132.32 -110.05 REMARK 500 ASP A 190 -175.18 -172.21 REMARK 500 LYS A 209 -7.66 67.58 REMARK 500 ASP A 246 -18.12 85.84 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 347 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 60 O REMARK 620 2 LEU A 62 O 100.2 REMARK 620 3 VAL A 65 O 92.7 86.5 REMARK 620 4 HOH A 415 O 98.8 85.4 166.9 REMARK 620 5 DC D 3 OP1 172.0 87.6 85.8 83.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 346 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 101 O REMARK 620 2 VAL A 103 O 92.4 REMARK 620 3 ILE A 106 O 89.1 86.6 REMARK 620 4 HOH A 402 O 79.5 89.4 167.8 REMARK 620 5 DG P 9 OP1 164.5 89.6 106.3 85.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 341 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 145 OD2 REMARK 620 2 HIS A 252 ND1 78.5 REMARK 620 3 HOH A 397 O 99.0 98.2 REMARK 620 4 HOH A 400 O 88.6 76.7 169.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 339 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 100.0 REMARK 620 3 DCP A 338 O1G 88.6 170.0 REMARK 620 4 DCP A 338 O2B 173.7 84.0 86.9 REMARK 620 5 DCP A 338 O1A 98.8 93.3 90.3 85.7 REMARK 620 6 HOH A 374 O 93.0 69.3 105.5 83.8 160.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 340 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD2 REMARK 620 2 ASP A 192 OD1 118.4 REMARK 620 3 ASP A 256 OD2 111.6 91.6 REMARK 620 4 DCP A 338 O1A 89.5 91.1 154.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 343 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DCP A 350 O3B REMARK 620 2 DCP A 350 O1A 71.3 REMARK 620 N 1 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 338 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DCP A 350 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 341 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 343 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 345 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 346 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 347 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 351 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 352 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 353 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 354 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 355 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN T 344 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN D 342 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RH4 RELATED DB: PDB REMARK 900 RELATED ID: 3RH6 RELATED DB: PDB DBREF 3RH5 A 1 335 UNP P06746 DPOLB_HUMAN 1 335 DBREF 3RH5 T 1 16 PDB 3RH5 3RH5 1 16 DBREF 3RH5 P 1 10 PDB 3RH5 3RH5 1 10 DBREF 3RH5 D 1 5 PDB 3RH5 3RH5 1 5 SEQADV 3RH5 ALA A 271 UNP P06746 TYR 271 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 ALA 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 SEQRES 1 T 16 DC DC DG DA DC DG DC 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 DDG SEQRES 1 D 5 DG DT DC DG DG MODRES 3RH5 DDG P 10 DG HET DDG P 10 21 HET DCP A 338 28 HET DCP A 350 28 HET MN A 339 1 HET MN A 340 1 HET MN A 341 1 HET MN A 343 1 HET MN A 345 1 HET NA A 346 1 HET NA A 347 1 HET CL A 351 1 HET CL A 352 1 HET CL A 353 1 HET CL A 354 1 HET CL A 355 1 HET MN T 344 1 HET MN D 342 1 HETNAM DDG 2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE HETNAM DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 3 DDG C10 H14 N5 O6 P FORMUL 5 DCP 2(C9 H16 N3 O13 P3) FORMUL 7 MN 7(MN 2+) FORMUL 12 NA 2(NA 1+) FORMUL 14 CL 5(CL 1-) FORMUL 21 HOH *286(H2 O) HELIX 1 1 ASN A 12 VAL A 29 1 18 HELIX 2 2 ALA A 32 TYR A 49 1 18 HELIX 3 3 SER A 55 LYS A 60 1 6 HELIX 4 4 GLY A 66 GLY A 80 1 15 HELIX 5 5 LEU A 82 ARG A 89 1 8 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 CYS A 178 ARG A 183 1 6 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 SER A 334 5 6 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 CYS A 239 O ARG A 253 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 O3' DG P 9 P DDG P 10 1555 1555 1.59 LINK O LYS A 60 NA NA A 347 1555 1555 2.72 LINK O LEU A 62 NA NA A 347 1555 1555 2.73 LINK O VAL A 65 NA NA A 347 1555 1555 2.59 LINK O THR A 101 NA NA A 346 1555 1555 2.52 LINK O VAL A 103 NA NA A 346 1555 1555 2.69 LINK O ILE A 106 NA NA A 346 1555 1555 2.65 LINK OD2 ASP A 145 MN MN A 341 1555 1555 2.31 LINK OD1 ASP A 190 MN MN A 339 1555 1555 2.17 LINK OD2 ASP A 190 MN MN A 340 1555 1555 2.16 LINK OD2 ASP A 192 MN MN A 339 1555 1555 2.20 LINK OD1 ASP A 192 MN MN A 340 1555 1555 2.18 LINK ND1 HIS A 252 MN MN A 341 1555 1555 2.64 LINK OD2 ASP A 256 MN MN A 340 1555 1555 2.28 LINK O1G DCP A 338 MN MN A 339 1555 1555 2.05 LINK O2B DCP A 338 MN MN A 339 1555 1555 2.10 LINK O1A DCP A 338 MN MN A 339 1555 1555 2.14 LINK O1A DCP A 338 MN MN A 340 1555 1555 2.49 LINK MN MN A 339 O HOH A 374 1555 1555 2.48 LINK MN MN A 341 O HOH A 397 1555 1555 2.55 LINK MN MN A 341 O HOH A 400 1555 1555 2.56 LINK MN MN A 343 O3B DCP A 350 1555 1555 2.37 LINK MN MN A 343 O1A DCP A 350 1555 1555 2.71 LINK NA NA A 346 O HOH A 402 1555 1555 2.98 LINK NA NA A 346 OP1 DG P 9 1555 1555 2.54 LINK NA NA A 347 O HOH A 415 1555 1555 2.77 LINK NA NA A 347 OP1 DC D 3 1555 1555 2.82 LINK N7 DG D 4 MN MN D 342 1555 1555 2.66 CISPEP 1 GLY A 274 SER A 275 0 3.42 SITE 1 AC1 20 GLY A 179 SER A 180 ARG A 183 GLY A 189 SITE 2 AC1 20 ASP A 190 ASP A 192 ALA A 271 PHE A 272 SITE 3 AC1 20 THR A 273 GLY A 274 ASP A 276 ASN A 279 SITE 4 AC1 20 MN A 339 MN A 340 MN A 345 HOH A 374 SITE 5 AC1 20 HOH A 380 HOH A 533 DDG P 10 DG T 6 SITE 1 AC2 9 ILE A 174 THR A 176 THR A 196 LYS A 262 SITE 2 AC2 9 TYR A 265 TYR A 266 MN A 343 HOH A 440 SITE 3 AC2 9 HOH A 529 SITE 1 AC3 5 ASP A 190 ASP A 192 DCP A 338 MN A 340 SITE 2 AC3 5 HOH A 374 SITE 1 AC4 5 ASP A 190 ASP A 192 ASP A 256 DCP A 338 SITE 2 AC4 5 MN A 339 SITE 1 AC5 4 ASP A 145 HIS A 252 HOH A 397 HOH A 400 SITE 1 AC6 1 DCP A 350 SITE 1 AC7 1 DCP A 338 SITE 1 AC8 5 THR A 101 VAL A 103 ILE A 106 HOH A 402 SITE 2 AC8 5 DG P 9 SITE 1 AC9 5 LYS A 60 LEU A 62 VAL A 65 HOH A 415 SITE 2 AC9 5 DC D 3 SITE 1 BC1 2 ASN A 294 THR A 297 SITE 1 BC2 3 LEU A 82 GLU A 86 ARG A 89 SITE 1 BC3 3 GLN A 159 VAL A 177 HOH A 422 SITE 1 BC4 2 PRO A 330 LYS A 331 SITE 1 BC5 4 ALA A 32 ILE A 33 HIS A 34 LYS A 35 SITE 1 BC6 2 DA T 4 DC T 5 SITE 1 BC7 1 DG D 4 CRYST1 51.220 79.920 55.090 90.00 107.93 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 0.019524 0.000000 0.006317 0.00000 SCALE2 0.000000 0.012513 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019079 0.00000