HEADER DNA 02-FEB-01 1I1P TITLE REFINEMENT INCLUDING EXPERIMENTAL MAD PHASES ALLOWS AN EXHAUSTIVE TITLE 2 STUDY OF ORDERED SOLVENT MOLECULES FOR A PLATINATED DECANUCLEOTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*AP*GP*AP*GP*CP*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 ANTITUMOR DRUG, CIS-DDP, INTERSTRAND CROSS-LINK, DEOXYRIBONUCLEIC KEYWDS 2 ACID, SPERMINE, DNA EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,W.SHEPARD,C.ZELWER REVDAT 5 07-FEB-24 1I1P 1 REMARK LINK REVDAT 4 13-JUL-11 1I1P 1 VERSN REVDAT 3 23-JUN-10 1I1P 1 HET REVDAT 2 24-FEB-09 1I1P 1 VERSN REVDAT 1 21-JUN-02 1I1P 0 JRNL AUTH F.COSTE,W.SHEPARD,C.ZELWER JRNL TITL DESCRIPTION OF ORDERED SOLVENT MOLECULES IN A PLATINATED JRNL TITL 2 DECANUCLEOTIDE DUPLEX REFINED AT 1.6A RESOLUTION AGAINST JRNL TITL 3 EXPERIMENTAL MAD PHASES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 58 431 2002 JRNL REFN ISSN 0907-4449 JRNL PMID 11856828 JRNL DOI 10.1107/S0907444901021709 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.COSTE,J.M.MALINGE,L.SERRE,W.SHEPARD,M.ROTH,M.LENG,C.ZELWER REMARK 1 TITL CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA CONTAINING A REMARK 1 TITL 2 CISPLATIN INTERSTRAND CROSS-LINK AT 1.63 ANGSTROM REMARK 1 TITL 3 RESOLUTION: HYDRATION AT THE PLATINATED SITE REMARK 1 REF NUCLEIC ACIDS RES. V. 27 1837 1999 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/27.8.1837 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 7322 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 404 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 135 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I1P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW21B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0906,1.0718,1.0711,1.0301 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7333 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE, NACL, KCL, REMARK 280 SPERMINE, MPD, PH 6.2, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K 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 21.44500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.99000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.44500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.99000 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 263 O HOH A 272 2.11 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 DC A 1 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 1 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC A 2 N3 - C4 - N4 ANGL. DEV. = 5.0 DEGREES REMARK 500 DC A 4 O3' - P - OP2 ANGL. DEV. = 19.6 DEGREES REMARK 500 DG A 5 O5' - C5' - C4' ANGL. DEV. = -6.8 DEGREES REMARK 500 DG A 5 C4 - C5 - N7 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 5 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG A 5 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 7 C6 - N1 - C2 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT A 7 C5 - C6 - N1 ANGL. DEV. = -4.7 DEGREES REMARK 500 DC A 8 O3' - P - OP2 ANGL. DEV. = 7.6 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 9 O3' - P - OP2 ANGL. DEV. = 7.8 DEGREES REMARK 500 DC A 10 O3' - P - OP2 ANGL. DEV. = 10.8 DEGREES REMARK 500 DA B 12 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA B 12 C6 - N1 - C2 ANGL. DEV. = 5.6 DEGREES REMARK 500 DA B 12 N1 - C2 - N3 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 12 N1 - C6 - N6 ANGL. DEV. = 3.8 DEGREES REMARK 500 DA B 14 OP1 - P - OP2 ANGL. DEV. = 9.8 DEGREES REMARK 500 DG B 15 O5' - C5' - C4' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = -5.5 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 SPM B 222 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 CPT A 221 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 N7 REMARK 620 2 CPT A 221 N1 90.5 REMARK 620 3 CPT A 221 N2 174.5 85.3 REMARK 620 4 DG B 15 N7 86.4 176.5 97.8 REMARK 620 N 1 2 3 DBREF 1I1P A 1 10 PDB 1I1P 1I1P 1 10 DBREF 1I1P B 11 20 PDB 1I1P 1I1P 11 20 SEQRES 1 A 10 DC DC DT DC DG DC DT DC DT DC SEQRES 1 B 10 DG DA DG DA DG DC DG DA DG DG HET CPT A 221 3 HET SPM B 222 12 HETNAM CPT CISPLATIN HETNAM SPM SPERMINE HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 3 CPT CL2 H6 N2 PT FORMUL 4 SPM C10 H26 N4 FORMUL 5 HOH *135(H2 O) LINK N7 DG A 5 PT1 CPT A 221 1555 1555 2.01 LINK PT1 CPT A 221 N7 DG B 15 1555 1555 1.99 SITE 1 AC1 8 DG A 5 DT A 7 DC A 8 HOH A 235 SITE 2 AC1 8 HOH A 249 HOH A 259 DG B 15 HOH B 233 SITE 1 AC2 6 DC A 2 DT A 3 DC B 16 DG B 17 SITE 2 AC2 6 HOH B 263 HOH B 269 CRYST1 42.890 29.980 46.570 90.00 95.98 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 0.023315 0.000000 0.002442 0.00000 SCALE2 0.000000 0.033356 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021591 0.00000