HEADER REPLICATION 15-JAN-18 6C59 TITLE CHIMERIC POL KAPPA RIR REV1 C-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHIMERIC POL KAPPA RIR REV1 C-TERMINAL DOMAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DINB PROTEIN,DINP,REV1-LIKE TERMINAL DEOXYCYTIDYL COMPND 5 TRANSFERASE; COMPND 6 EC: 2.7.7.7,2.7.7.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: POLK, DINB1, REV1, REV1L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSLESION SYNTHESIS, DNA DAMAGE TOLERANCE, REPLICATION EXPDTA X-RAY DIFFRACTION AUTHOR J.L.WOJTASZEK,P.ZHOU REVDAT 5 04-OCT-23 6C59 1 REMARK REVDAT 4 04-DEC-19 6C59 1 REMARK REVDAT 3 10-JUL-19 6C59 1 JRNL REVDAT 2 26-JUN-19 6C59 1 JRNL REVDAT 1 12-JUN-19 6C59 0 JRNL AUTH J.L.WOJTASZEK,N.CHATTERJEE,J.NAJEEB,A.RAMOS,M.LEE,K.BIAN, JRNL AUTH 2 J.Y.XUE,B.A.FENTON,H.PARK,D.LI,M.T.HEMANN,J.HONG,G.C.WALKER, JRNL AUTH 3 P.ZHOU JRNL TITL A SMALL MOLECULE TARGETING MUTAGENIC TRANSLESION SYNTHESIS JRNL TITL 2 IMPROVES CHEMOTHERAPY. JRNL REF CELL V. 178 152 2019 JRNL REFN ISSN 1097-4172 JRNL PMID 31178121 JRNL DOI 10.1016/J.CELL.2019.05.028 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 7025 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.730 REMARK 3 FREE R VALUE TEST SET COUNT : 332 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 33.3941 - 2.5576 1.00 3451 164 0.1823 0.2061 REMARK 3 2 2.5576 - 2.0301 1.00 3242 168 0.1902 0.2474 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.850 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 889 REMARK 3 ANGLE : 0.729 1196 REMARK 3 CHIRALITY : 0.045 136 REMARK 3 PLANARITY : 0.005 151 REMARK 3 DIHEDRAL : 2.346 543 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 6C59 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000232078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7068 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 41.773 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.340 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: 4FJO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH 7.2, KCL, CHAPS, TCEP, SODIUM REMARK 280 ACETATE, PEG 4000, ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.79500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.61000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.19250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.61000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.61000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.39750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.61000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.61000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.19250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.61000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.61000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.39750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.79500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 333 LIES ON A SPECIAL POSITION. 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 SER A 1 REMARK 465 HIS A 2 REMARK 465 MET A 3 REMARK 465 ILE A 15 REMARK 465 SER A 16 REMARK 465 ASN A 17 REMARK 465 GLY A 18 REMARK 465 THR A 115 REMARK 465 LEU A 116 REMARK 465 LYS A 117 REMARK 465 VAL A 118 REMARK 465 THR A 119 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 53 CG CD OE1 OE2 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 70 59.51 -93.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 201 DBREF 6C59 A 4 17 UNP Q9QUG2 POLK_MOUSE 564 577 DBREF 6C59 A 20 119 UNP Q920Q2 REV1_MOUSE 1150 1249 SEQADV 6C59 SER A 1 UNP Q9QUG2 EXPRESSION TAG SEQADV 6C59 HIS A 2 UNP Q9QUG2 EXPRESSION TAG SEQADV 6C59 MET A 3 UNP Q9QUG2 EXPRESSION TAG SEQADV 6C59 GLY A 18 UNP Q9QUG2 LINKER SEQADV 6C59 GLY A 19 UNP Q9QUG2 LINKER SEQRES 1 A 119 SER HIS MET LYS SER PHE PHE ASP LYS LYS ARG SER GLU SEQRES 2 A 119 ARG ILE SER ASN GLY GLY PHE ARG PRO ALA ALA PRO ASN SEQRES 3 A 119 LEU ALA GLY ALA VAL GLU PHE SER ASP VAL LYS THR LEU SEQRES 4 A 119 LEU LYS GLU TRP ILE THR THR ILE SER ASP PRO MET GLU SEQRES 5 A 119 GLU ASP ILE LEU GLN VAL VAL ARG TYR CYS THR ASP LEU SEQRES 6 A 119 ILE GLU GLU LYS ASP LEU GLU LYS LEU ASP LEU VAL ILE SEQRES 7 A 119 LYS TYR MET LYS ARG LEU MET GLN GLN SER VAL GLU SER SEQRES 8 A 119 VAL TRP ASN MET ALA PHE ASP PHE ILE LEU ASP ASN VAL SEQRES 9 A 119 GLN VAL VAL LEU GLN GLN THR TYR GLY SER THR LEU LYS SEQRES 10 A 119 VAL THR HET ACT A 201 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *70(H2 O) HELIX 1 AA1 SER A 5 ARG A 14 1 10 HELIX 2 AA2 GLU A 32 ILE A 47 1 16 HELIX 3 AA3 MET A 51 GLU A 68 1 18 HELIX 4 AA4 ASP A 70 SER A 88 1 19 HELIX 5 AA5 GLU A 90 GLY A 113 1 24 SITE 1 AC1 2 HOH A 305 HOH A 334 CRYST1 47.220 47.220 89.590 90.00 90.00 90.00 P 43 21 2 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 0.021177 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011162 0.00000