HEADER DNA 17-JAN-07 2OKS TITLE X-RAY STRUCTURE OF A DNA REPAIR SUBSTRATE CONTAINING AN ALKYL TITLE 2 INTERSTRAND CROSSLINK AT 1.65 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*(C34)P*GP*TP*TP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N4C-ETHYL-N4C CROSSLINKED DNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS OF DNA OLIGO, CROSSLINK SOURCE 4 PHOSPHORAMIDITE SYNTHESIZED SEPARATELY KEYWDS INTERSTRAND CROSSLINK, DNA, DNA DAMAGE EXPDTA X-RAY DIFFRACTION AUTHOR M.C.SWENSON,S.R.PARANAWITHANA,P.S.MILLER,C.L.KIELKOPF REVDAT 5 30-AUG-23 2OKS 1 REMARK LINK REVDAT 4 30-JUL-14 2OKS 1 ATOM HETATM VERSN REVDAT 3 24-FEB-09 2OKS 1 VERSN REVDAT 2 24-APR-07 2OKS 1 JRNL REVDAT 1 13-FEB-07 2OKS 0 JRNL AUTH M.C.SWENSON,S.R.PARANAWITHANA,P.S.MILLER,C.L.KIELKOPF JRNL TITL STRUCTURE OF A DNA REPAIR SUBSTRATE CONTAINING AN ALKYL JRNL TITL 2 INTERSTRAND CROSS-LINK AT 1.65 A RESOLUTION. JRNL REF BIOCHEMISTRY V. 46 4545 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17375936 JRNL DOI 10.1021/BI700109R REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 992530.750 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.1 REMARK 3 NUMBER OF REFLECTIONS : 2924 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.500 REMARK 3 FREE R VALUE TEST SET COUNT : 162 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.016 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 403 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 27 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.044 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 203 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.86000 REMARK 3 B22 (A**2) : 0.62000 REMARK 3 B33 (A**2) : 0.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.75000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 2.140 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC INDIVIDUAL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.890 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 25.63 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : XLINK2.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : XLINK2.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2OKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-07. REMARK 100 THE DEPOSITION ID IS D_1000041259. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 200 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : MIRRORS, GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2924 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04600 REMARK 200 FOR THE DATA SET : 38.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.56 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.04700 REMARK 200 FOR SHELL : 25.70 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1EN8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PURIFIED CROSSLINKED DNA WAS REMARK 280 DISSOLVED IN A BUFFER CONTAINING 22 MM AMMONIUM ACETATE, 11 MM REMARK 280 TRIS-HYDROXYMETHYL-AMINOMETHANE (TRIS)-HCL PH 8.0, AND 11 MM REMARK 280 CALCIUM ACETATE. CRYSTALS WERE GROWN USING THE SITTING DROP REMARK 280 VAPOR DIFFUSION METHOD AT 277K, IN WHICH 3 UL OF A RESERVOIR REMARK 280 SOLUTION CONTAINING 27% 2-3 METHYL-PENTADIOL, 115 MM CALCIUM REMARK 280 ACETATE, AND 10 MM TRIS-HCL PH 8.0 WAS ADDED TO AN EQUAL VOLUME REMARK 280 OF DNA SOLUTION, AND THE MIXTURE WAS EQUILIBRATED AGAINST 700 UL REMARK 280 OF THE RESERVOIR SOLUTION. CRYSTALS FIRST APPEARED AFTER TWO REMARK 280 WEEKS. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 15.93500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.44500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 15.93500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.44500 REMARK 290 SMTRY3 4 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 DOUBLE-STRANDED DNA GENERATED REMARK 300 BY THE CRYSTALLOGRAPHIC TWO-FOLD AXIS 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: DIMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 17.62529 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 31.25717 REMARK 600 REMARK 600 HETEROGEN REMARK 600 THIS IS A N4C-ETHYL-N4C CROSSLINKED DNA. REMARK 600 ONLY HALF OF THE ETHYL LINKER IS PRESENT IN THE REMARK 600 COORDINATES SINCE IT IS LOCATED ON THE TWO-FOLD AXES. 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 CA A 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 OP2 REMARK 620 2 DT A 7 OP1 177.5 REMARK 620 3 HOH A 214 O 91.5 85.9 REMARK 620 4 HOH A 215 O 88.0 92.4 96.2 REMARK 620 5 HOH A 216 O 94.7 85.1 88.9 174.2 REMARK 620 6 HOH A 217 O 99.8 82.7 168.3 87.1 87.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 9 N7 REMARK 620 2 DG A 10 O6 72.0 REMARK 620 3 HOH A 209 O 126.3 54.8 REMARK 620 4 HOH A 209 O 116.1 53.0 21.8 REMARK 620 5 HOH A 210 O 80.3 149.3 147.4 135.8 REMARK 620 6 HOH A 211 O 160.2 105.9 57.6 74.0 104.6 REMARK 620 7 HOH A 212 O 83.3 92.1 103.7 124.0 97.4 77.0 REMARK 620 8 HOH A 213 O 88.4 79.9 76.8 55.4 86.7 110.9 170.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 201 O REMARK 620 2 HOH A 201 O 81.7 REMARK 620 3 HOH A 202 O 80.4 131.9 REMARK 620 4 HOH A 203 O 157.5 100.2 81.9 REMARK 620 5 HOH A 204 O 100.2 144.8 82.4 91.1 REMARK 620 6 HOH A 204 O 130.9 73.2 146.2 70.0 79.8 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 CA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EN8 RELATED DB: PDB REMARK 900 AN UNCROSSLINKED DNA DUPLEX OF IDENTICAL SEQUENCE WITHOUT AN REMARK 900 INTERSTRAND CROSSLINK. DBREF 2OKS A 1 10 PDB 2OKS 2OKS 1 10 SEQRES 1 A 10 DC DC DA DA C34 DG DT DT DG DG MODRES 2OKS C34 A 5 DC HET C34 A 5 20 HET CA A 101 1 HET CA A 102 1 HET CA A 103 1 HETNAM C34 N4-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM CA CALCIUM ION FORMUL 1 C34 C10 H16 N3 O7 P FORMUL 2 CA 3(CA 2+) FORMUL 5 HOH *75(H2 O) LINK O3' DA A 4 P C34 A 5 1555 1555 1.60 LINK C7 C34 A 5 C7 C34 A 5 1555 2656 1.57 LINK O3' C34 A 5 P DG A 6 1555 1555 1.63 LINK OP2 DG A 6 CA CA A 103 4646 1555 2.44 LINK OP1 DT A 7 CA CA A 103 1555 1555 2.44 LINK N7 DG A 9 CA CA A 102 1555 1555 2.67 LINK O6 DG A 10 CA CA A 102 1555 1555 2.95 LINK CA CA A 101 O HOH A 201 1555 4555 2.19 LINK CA CA A 101 O HOH A 201 1555 3555 2.70 LINK CA CA A 101 O HOH A 202 1555 1555 2.47 LINK CA CA A 101 O HOH A 203 1555 1555 2.51 LINK CA CA A 101 O HOH A 204 1555 1555 2.21 LINK CA CA A 101 O HOH A 204 1555 2655 2.95 LINK CA CA A 102 O HOH A 209 1555 1555 2.77 LINK CA CA A 102 O HOH A 209 1555 2655 3.10 LINK CA CA A 102 O HOH A 210 1555 1555 2.06 LINK CA CA A 102 O HOH A 211 1555 1555 2.32 LINK CA CA A 102 O HOH A 212 1555 1555 3.13 LINK CA CA A 102 O HOH A 213 1555 1555 2.72 LINK CA CA A 103 O HOH A 214 1555 1555 2.39 LINK CA CA A 103 O HOH A 215 1555 1555 2.51 LINK CA CA A 103 O HOH A 216 1555 1555 2.46 LINK CA CA A 103 O HOH A 217 1555 1555 2.46 SITE 1 AC1 4 HOH A 201 HOH A 202 HOH A 203 HOH A 204 SITE 1 AC2 6 DG A 9 DG A 10 HOH A 209 HOH A 210 SITE 2 AC2 6 HOH A 211 HOH A 213 SITE 1 AC3 6 DG A 6 DT A 7 HOH A 214 HOH A 215 SITE 2 AC3 6 HOH A 216 HOH A 217 CRYST1 31.870 24.890 34.350 90.00 114.50 90.00 C 1 2 1 4 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 0.031377 0.000000 0.014300 0.00000 SCALE2 0.000000 0.040177 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031993 0.00000