HEADER TRANSFERASE/DNA 15-OCT-19 6UOM TITLE Y271G DNA POLYMERASE BETA TERNARY COMPLEX WITH TEMPLATING ADENINE AND TITLE 2 INCOMING R8-OXO-GTP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)- COMPND 3 3'); COMPND 4 CHAIN: T; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*G)-3'); COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(P*GP*TP*CP*GP*G)-3'); COMPND 12 CHAIN: D; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: DNA POLYMERASE BETA; COMPND 16 CHAIN: A; COMPND 17 EC: 2.7.7.7,4.2.99.-; COMPND 18 ENGINEERED: YES; COMPND 19 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 4; SOURCE 14 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 15 ORGANISM_COMMON: HUMAN; SOURCE 16 ORGANISM_TAXID: 9606; SOURCE 17 GENE: POLB; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DNA POLYMERASE, OXIDIZED RIBONUCLEOTIDE, DNA DAMAGE, DNA BINDING KEYWDS 2 PROTEIN, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SMITH,B.D.FREUDENTHAL REVDAT 4 11-OCT-23 6UOM 1 LINK REVDAT 3 19-FEB-20 6UOM 1 JRNL REVDAT 2 15-JAN-20 6UOM 1 JRNL REVDAT 1 08-JAN-20 6UOM 0 JRNL AUTH M.R.SMITH,K.S.ALNAJJAR,N.M.HOITSMA,J.B.SWEASY, JRNL AUTH 2 B.D.FREUDENTHAL JRNL TITL MOLECULAR AND STRUCTURAL CHARACTERIZATION OF OXIDIZED JRNL TITL 2 RIBONUCLEOTIDE INSERTION INTO DNA BY HUMAN DNA POLYMERASE JRNL TITL 3 BETA. JRNL REF J.BIOL.CHEM. V. 295 1613 2020 JRNL REFN ESSN 1083-351X JRNL PMID 31892517 JRNL DOI 10.1074/JBC.RA119.011569 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 71.4 REMARK 3 NUMBER OF REFLECTIONS : 37845 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 3769 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 25.0000 - 6.0989 0.87 1533 176 0.1526 0.1558 REMARK 3 2 6.0989 - 4.8523 0.95 1689 180 0.1483 0.1922 REMARK 3 3 4.8523 - 4.2423 0.96 1681 190 0.1373 0.2177 REMARK 3 4 4.2423 - 3.8560 0.96 1730 176 0.1399 0.1886 REMARK 3 5 3.8560 - 3.5804 0.97 1755 175 0.1621 0.2168 REMARK 3 6 3.5804 - 3.3698 0.97 1707 177 0.1672 0.2099 REMARK 3 7 3.3698 - 3.2014 0.97 1738 182 0.1818 0.2314 REMARK 3 8 3.2014 - 3.0623 0.97 1689 199 0.2241 0.2953 REMARK 3 9 3.0623 - 2.9446 0.95 1708 175 0.2581 0.3082 REMARK 3 10 2.9446 - 2.8432 0.94 1627 215 0.2599 0.3144 REMARK 3 11 2.8432 - 2.7544 0.93 1647 176 0.2495 0.3002 REMARK 3 12 2.7544 - 2.6757 0.89 1561 176 0.2426 0.2801 REMARK 3 13 2.6757 - 2.6054 0.85 1537 141 0.2483 0.3111 REMARK 3 14 2.6054 - 2.5419 0.83 1437 170 0.2535 0.2620 REMARK 3 15 2.5419 - 2.4841 0.77 1395 144 0.2550 0.3103 REMARK 3 16 2.4841 - 2.4313 0.71 1225 136 0.2557 0.3402 REMARK 3 17 2.4313 - 2.3827 0.68 1217 146 0.2570 0.3272 REMARK 3 18 2.3827 - 2.3378 0.64 1115 134 0.2512 0.2887 REMARK 3 19 2.3378 - 2.2961 0.61 1072 135 0.2530 0.2929 REMARK 3 20 2.2961 - 2.2572 0.58 1040 112 0.2485 0.2923 REMARK 3 21 2.2572 - 2.2208 0.53 896 96 0.2546 0.3061 REMARK 3 22 2.2208 - 2.1866 0.47 867 96 0.2733 0.3445 REMARK 3 23 2.1866 - 2.1545 0.40 699 79 0.2646 0.2685 REMARK 3 24 2.1545 - 2.1242 0.32 551 60 0.2511 0.2582 REMARK 3 25 2.1242 - 2.0955 0.28 498 59 0.2677 0.3731 REMARK 3 26 2.0955 - 2.0683 0.21 369 58 0.2663 0.2364 REMARK 3 27 2.0683 - 2.0500 0.05 93 6 0.2434 0.2012 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.290 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.15 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6UOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1000243695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-19 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37845 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 25.088 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX 1.14_3260 REMARK 200 STARTING MODEL: 2FMS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM IMIDAZOLE, 350 MM SODIUM REMARK 280 CHLORIDE, 19% PEG3350, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 206 CG CD CE NZ REMARK 470 GLN A 207 CG CD OE1 NE2 REMARK 470 LYS A 209 CG CD CE NZ 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 170 113.48 -167.21 REMARK 500 SER A 171 -9.14 -57.58 REMARK 500 CYS A 178 -133.79 -121.71 REMARK 500 ASP A 246 -20.75 85.09 REMARK 500 SER A 275 -179.24 -68.69 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 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG P 9 OP1 REMARK 620 2 HOH P 208 O 97.6 REMARK 620 3 THR A 101 O 171.5 76.4 REMARK 620 4 VAL A 103 O 94.6 164.9 92.3 REMARK 620 5 ILE A 106 O 93.9 85.1 91.6 85.3 REMARK 620 6 HOH A 645 O 88.2 94.7 86.4 94.5 177.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH P 207 O REMARK 620 2 ASP A 190 OD2 77.8 REMARK 620 3 ASP A 192 OD1 168.0 101.1 REMARK 620 4 8GT A 407 O2A 94.8 70.5 96.0 REMARK 620 N 1 2 3 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 DC D 3 OP1 REMARK 620 2 HOH D 205 O 75.1 REMARK 620 3 HOH D 212 O 86.4 76.3 REMARK 620 4 LYS A 60 O 172.8 97.8 93.0 REMARK 620 5 LEU A 62 O 95.8 165.7 92.4 91.4 REMARK 620 6 VAL A 65 O 89.2 96.0 171.9 90.5 94.8 REMARK 620 N 1 2 3 4 5 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 HOH D 202 O REMARK 620 2 ASP A 145 OD2 161.5 REMARK 620 3 HOH A 586 O 82.5 79.1 REMARK 620 4 HOH A 594 O 92.8 85.1 78.5 REMARK 620 5 HOH A 649 O 81.7 98.4 95.1 172.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 190 OD1 REMARK 620 2 ASP A 192 OD2 102.4 REMARK 620 3 8GT A 407 O1B 161.9 92.9 REMARK 620 4 8GT A 407 O1G 82.0 172.5 81.8 REMARK 620 5 8GT A 407 O2A 90.2 106.6 94.7 79.2 REMARK 620 6 HOH A 533 O 86.3 86.3 85.0 87.9 167.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 8GT A 407 O2G REMARK 620 2 HOH A 648 O 97.9 REMARK 620 3 HOH A 653 O 103.4 73.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO T 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DOC P 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8GT A 407 DBREF 6UOM T 1 16 PDB 6UOM 6UOM 1 16 DBREF 6UOM P 1 9 PDB 6UOM 6UOM 1 9 DBREF 6UOM D 1 5 PDB 6UOM 6UOM 1 5 DBREF 6UOM A 1 335 UNP P06746 DPOLB_HUMAN 1 335 SEQADV 6UOM GLY A 271 UNP P06746 TYR 271 ENGINEERED MUTATION SEQRES 1 T 16 DC DC DG DA DC DA DG DC DG DC DA DT DC SEQRES 2 T 16 DA DG DC SEQRES 1 P 9 DG DC DT DG DA DT DG DC DG 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 GLY 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 EDO T 101 10 HET DOC P 101 18 HET EDO D 101 10 HET NA A 401 1 HET NA A 402 1 HET MN A 403 1 HET MN A 404 1 HET NA A 405 1 HET NA A 406 1 HET 8GT A 407 45 HETNAM EDO 1,2-ETHANEDIOL HETNAM DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE HETNAM NA SODIUM ION HETNAM MN MANGANESE (II) ION HETNAM 8GT 8-OXO-GUANOSINE-5'-TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 2(C2 H6 O2) FORMUL 6 DOC C9 H14 N3 O6 P FORMUL 8 NA 4(NA 1+) FORMUL 10 MN 2(MN 2+) FORMUL 14 8GT C10 H16 N5 O15 P3 FORMUL 15 HOH *223(H2 O) HELIX 1 AA1 ASN A 12 VAL A 29 1 18 HELIX 2 AA2 ALA A 32 TYR A 49 1 18 HELIX 3 AA3 SER A 55 LYS A 61 1 7 HELIX 4 AA4 GLY A 66 GLY A 80 1 15 HELIX 5 AA5 LEU A 82 ASP A 91 1 10 HELIX 6 AA6 ASP A 91 THR A 101 1 11 HELIX 7 AA7 GLY A 107 GLU A 117 1 11 HELIX 8 AA8 THR A 121 ASN A 128 1 8 HELIX 9 AA9 GLU A 129 LEU A 132 5 4 HELIX 10 AB1 ASN A 133 TYR A 142 1 10 HELIX 11 AB2 TYR A 142 GLU A 147 1 6 HELIX 12 AB3 ARG A 152 ASP A 170 1 19 HELIX 13 AB4 CYS A 178 ARG A 183 1 6 HELIX 14 AB5 LYS A 209 VAL A 221 1 13 HELIX 15 AB6 PRO A 261 ASP A 263 5 3 HELIX 16 AB7 GLN A 264 GLY A 274 1 11 HELIX 17 AB8 SER A 275 LYS A 289 1 15 HELIX 18 AB9 SER A 315 ILE A 323 1 9 HELIX 19 AC1 GLU A 329 ARG A 333 5 5 SHEET 1 AA1 2 ILE A 150 PRO A 151 0 SHEET 2 AA1 2 SER A 187 SER A 188 -1 O SER A 188 N ILE A 150 SHEET 1 AA2 5 ILE A 174 VAL A 177 0 SHEET 2 AA2 5 MET A 191 THR A 196 -1 O LEU A 194 N THR A 176 SHEET 3 AA2 5 ARG A 253 LEU A 259 1 O ARG A 258 N LEU A 195 SHEET 4 AA2 5 LYS A 234 CYS A 239 -1 N PHE A 235 O ILE A 257 SHEET 5 AA2 5 ILE A 224 LYS A 230 -1 N LEU A 228 O MET A 236 SHEET 1 AA3 2 PHE A 200 THR A 201 0 SHEET 2 AA3 2 SER A 204 THR A 205 -1 O SER A 204 N THR A 201 SHEET 1 AA4 2 PHE A 291 ILE A 293 0 SHEET 2 AA4 2 ILE A 298 PRO A 300 -1 O ARG A 299 N THR A 292 LINK O3' DG P 9 P DOC P 101 1555 1555 1.55 LINK OP1 DG P 9 NA NA A 401 1555 1555 2.34 LINK O HOH P 207 MN MN A 404 1555 1555 2.01 LINK O HOH P 208 NA NA A 401 1555 1555 2.54 LINK OP1 DC D 3 NA NA A 402 1555 1555 2.54 LINK O HOH D 202 NA NA A 405 1556 1555 2.25 LINK O HOH D 205 NA NA A 402 1555 1555 2.60 LINK O HOH D 212 NA NA A 402 1555 1555 2.51 LINK O LYS A 60 NA NA A 402 1555 1555 2.38 LINK O LEU A 62 NA NA A 402 1555 1555 2.41 LINK O VAL A 65 NA NA A 402 1555 1555 2.41 LINK O THR A 101 NA NA A 401 1555 1555 2.25 LINK O VAL A 103 NA NA A 401 1555 1555 2.58 LINK O ILE A 106 NA NA A 401 1555 1555 2.48 LINK OD2 ASP A 145 NA NA A 405 1555 1555 2.14 LINK OD1 ASP A 190 MN MN A 403 1555 1555 2.08 LINK OD2 ASP A 190 MN MN A 404 1555 1555 2.50 LINK OD2 ASP A 192 MN MN A 403 1555 1555 2.10 LINK OD1 ASP A 192 MN MN A 404 1555 1555 1.99 LINK NA NA A 401 O HOH A 645 1555 1555 2.57 LINK MN MN A 403 O1B 8GT A 407 1555 1555 2.24 LINK MN MN A 403 O1G 8GT A 407 1555 1555 2.40 LINK MN MN A 403 O2A 8GT A 407 1555 1555 2.12 LINK MN MN A 403 O HOH A 533 1555 1555 2.36 LINK MN MN A 404 O2A 8GT A 407 1555 1555 2.75 LINK NA NA A 405 O HOH A 586 1555 1555 2.23 LINK NA NA A 405 O HOH A 594 1555 1555 2.26 LINK NA NA A 405 O HOH A 649 1555 1555 2.37 LINK NA NA A 406 O2G 8GT A 407 1555 1555 2.42 LINK NA NA A 406 O HOH A 648 1555 1555 2.37 LINK NA NA A 406 O HOH A 653 1555 1555 2.36 CISPEP 1 GLY A 274 SER A 275 0 3.44 SITE 1 AC1 2 DT D 2 DG T 3 SITE 1 AC2 9 ARG A 254 8GT A 407 HOH A 564 DG P 9 SITE 2 AC2 9 HOH P 205 HOH P 207 HOH P 212 DA T 6 SITE 3 AC2 9 DG T 7 SITE 1 AC3 5 LYS A 35 LYS A 68 DG D 1 HOH D 207 SITE 2 AC3 5 HOH D 211 SITE 1 AC4 6 THR A 101 VAL A 103 ILE A 106 HOH A 645 SITE 2 AC4 6 DG P 9 HOH P 208 SITE 1 AC5 6 LYS A 60 LEU A 62 VAL A 65 DC D 3 SITE 2 AC5 6 HOH D 205 HOH D 212 SITE 1 AC6 5 ASP A 190 ASP A 192 MN A 404 8GT A 407 SITE 2 AC6 5 HOH A 533 SITE 1 AC7 6 ASP A 190 ASP A 192 ASP A 256 MN A 403 SITE 2 AC7 6 8GT A 407 HOH P 207 SITE 1 AC8 6 ASP A 145 HIS A 252 HOH A 586 HOH A 594 SITE 2 AC8 6 HOH A 649 HOH D 202 SITE 1 AC9 3 8GT A 407 HOH A 648 HOH A 653 SITE 1 AD1 20 ARG A 149 GLY A 179 SER A 180 ARG A 183 SITE 2 AD1 20 SER A 188 GLY A 189 ASP A 190 ASP A 192 SITE 3 AD1 20 GLY A 271 PHE A 272 THR A 273 GLY A 274 SITE 4 AD1 20 ASP A 276 ASN A 279 MN A 403 MN A 404 SITE 5 AD1 20 NA A 406 HOH A 628 DOC P 101 DA T 6 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