HEADER DNA 19-APR-01 1IHH TITLE 2.4 ANGSTROM CRYSTAL STRUCTURE OF AN OXALIPLATIN 1,2-D(GPG) TITLE 2 INTRASTRAND CROSS-LINK IN A DNA DODECAMER DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS RIGHT HANDED DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, OXALIPLATIN, KEYWDS 2 MODIFIED, DEOXYNUCLEIC ACID, DNA EXPDTA X-RAY DIFFRACTION AUTHOR B.SPINGLER,D.A.WHITTINGTON,S.J.LIPPARD REVDAT 4 07-FEB-24 1IHH 1 REMARK LINK REVDAT 3 24-JUL-19 1IHH 1 REMARK REVDAT 2 24-FEB-09 1IHH 1 VERSN REVDAT 1 26-OCT-01 1IHH 0 JRNL AUTH B.SPINGLER,D.A.WHITTINGTON,S.J.LIPPARD JRNL TITL 2.4 A CRYSTAL STRUCTURE OF AN OXALIPLATIN 1,2-D(GPG) JRNL TITL 2 INTRASTRAND CROSS-LINK IN A DNA DODECAMER DUPLEX. JRNL REF INORG.CHEM. V. 40 5596 2001 JRNL REFN ISSN 0020-1669 JRNL PMID 11599959 JRNL DOI 10.1021/IC010790T REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.230 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 487 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6296 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.209 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 631 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 4935 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 486 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 508.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2052 REMARK 3 NUMBER OF RESTRAINTS : 2360 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.021 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.106 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.001 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.006 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IHH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-01. REMARK 100 THE DEPOSITION ID IS D_1000013271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-00; 10-FEB-00 REMARK 200 TEMPERATURE (KELVIN) : 103; 173 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : SSRL; APS REMARK 200 BEAMLINE : BL9-1; 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.970; REMARK 200 1.0721,1.0724,1.0277,1.1206 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6296 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 9.760 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, SODIUM CACODYLATE, SPERMINE*4HCL, REMARK 280 BACL2, ETHYL ACETATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 20.97100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.62300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.52450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.97100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.62300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.52450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.97100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 25.62300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.52450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.97100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 25.62300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.52450 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 2 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DG B 4 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA B 8 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 DA B 8 C5' - C4' - C3' ANGL. DEV. = 7.8 DEGREES REMARK 500 DA B 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 10 O4' - C1' - N9 ANGL. DEV. = -4.5 DEGREES REMARK 500 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES 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 PT A 41 PT REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 6 N7 REMARK 620 2 DG A 6 O6 60.9 REMARK 620 3 DG A 7 N7 98.4 77.7 REMARK 620 4 DG A 7 O6 112.4 51.6 65.4 REMARK 620 5 DNH A 40 N1 155.0 104.6 97.8 58.6 REMARK 620 6 DNH A 40 N2 79.6 100.8 177.9 114.9 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 BA B 42 BA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DA B 10 N7 REMARK 620 2 DG B 11 O6 90.2 REMARK 620 3 DG B 11 N7 69.3 65.9 REMARK 620 4 HOH B 107 O 137.4 86.1 70.6 REMARK 620 N 1 2 3 DBREF 1IHH A 1 12 PDB 1IHH 1IHH 1 12 DBREF 1IHH B 1 12 PDB 1IHH 1IHH 1 12 SEQRES 1 A 12 DC DC DT DC DT DG DG DT DC DT DC DC SEQRES 1 B 12 DG DG DA DG DA DC DC DA DG DA DG DG HET PT A 41 1 HET DNH A 40 8 HET BA B 42 1 HETNAM PT PLATINUM (II) ION HETNAM DNH 1R,2R-DIAMINOCYCLOHEXANE HETNAM BA BARIUM ION FORMUL 3 PT PT 2+ FORMUL 4 DNH C6 H14 N2 FORMUL 5 BA BA 2+ FORMUL 6 HOH *12(H2 O) LINK N7 DG A 6 PT PT A 41 1555 1555 1.98 LINK O6 DG A 6 PT PT A 41 1555 1555 3.57 LINK N7 DG A 7 PT PT A 41 1555 1555 1.95 LINK O6 DG A 7 PT PT A 41 1555 1555 3.40 LINK N1 DNH A 40 PT PT A 41 1555 1555 2.03 LINK N2 DNH A 40 PT PT A 41 1555 1555 2.04 LINK N7 DA B 10 BA BA B 42 1555 1555 3.11 LINK O6 DG B 11 BA BA B 42 1555 1555 3.10 LINK N7 DG B 11 BA BA B 42 1555 1555 2.56 LINK BA BA B 42 O HOH B 107 1555 1555 3.04 SITE 1 AC1 3 DG A 6 DG A 7 DNH A 40 SITE 1 AC2 3 DA B 10 DG B 11 HOH B 107 SITE 1 AC3 4 DT A 5 DG A 6 DG A 7 PT A 41 CRYST1 41.942 51.246 87.049 90.00 90.00 90.00 I 2 2 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 0.023842 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019514 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011488 0.00000