HEADER DNA 05-JAN-98 1A2E TITLE CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA DECAMER CONTAINING A TITLE 2 CISPLATIN INTERSTRAND CROSS-LINK ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*TP*CP*GP*CP*TP*CP*TP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PT(CPT) CROSSLINKS N7(G5) AND N7(G15); COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*AP*GP*AP*GP*CP*GP*AP*GP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: PT(CPT) CROSSLINKS N7(G5) AND N7(G15) 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, DNA EXPDTA X-RAY DIFFRACTION AUTHOR F.COSTE,C.ZELWER REVDAT 6 07-FEB-24 1A2E 1 REMARK LINK REVDAT 5 13-JUL-11 1A2E 1 VERSN REVDAT 4 23-JUN-10 1A2E 1 FORMUL REVDAT 3 24-FEB-09 1A2E 1 VERSN REVDAT 2 01-APR-03 1A2E 1 JRNL REVDAT 1 12-APR-99 1A2E 0 JRNL AUTH F.COSTE,J.M.MALINGE,L.SERRE,W.SHEPARD,M.ROTH,M.LENG,C.ZELWER JRNL TITL CRYSTAL STRUCTURE OF A DOUBLE-STRANDED DNA CONTAINING A JRNL TITL 2 CISPLATIN INTERSTRAND CROSS-LINK AT 1.63 A RESOLUTION: JRNL TITL 3 HYDRATION AT THE PLATINATED SITE. JRNL REF NUCLEIC ACIDS RES. V. 27 1837 1999 JRNL REFN ISSN 0305-1048 JRNL PMID 10101191 JRNL DOI 10.1093/NAR/27.8.1837 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-96 REMARK 3 AUTHORS : G.M.SHELDRICK 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)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.1 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.169 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.169 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 340 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6983 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)) : 0.167 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 334 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6758 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 : 3 REMARK 3 SOLVENT ATOMS : 92 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 479.67 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2176 REMARK 3 NUMBER OF RESTRAINTS : 2201 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.062 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.098 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-223 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NUCLSQ REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A2E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000170308. 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) : 100.00 REMARK 200 PH : 6.20 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) : 1.0711 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS 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 : 7353 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 REMARK 200 RESOLUTION RANGE LOW (A) : 46.130 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) : 0.03700 REMARK 200 FOR THE DATA SET : 6.0000 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.06300 REMARK 200 R SYM FOR SHELL (I) : 0.04900 REMARK 200 FOR SHELL : 12.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.20 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA B 14 O4' DA B 14 C1' 0.069 REMARK 500 DG B 17 O4' DG B 17 C1' 0.077 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 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 2 O4' - C4' - C3' ANGL. DEV. = -3.0 DEGREES REMARK 500 DC A 2 C5 - C6 - N1 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 3 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DC A 4 O5' - C5' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DC A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 5 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = -6.7 DEGREES REMARK 500 DC A 6 C3' - O3' - P ANGL. DEV. = 10.1 DEGREES REMARK 500 DT A 7 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = -6.1 DEGREES REMARK 500 DT A 9 O4' - C4' - C3' ANGL. DEV. = -3.1 DEGREES REMARK 500 DC A 10 O4' - C4' - C3' ANGL. DEV. = -4.7 DEGREES REMARK 500 DG B 11 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DG B 11 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 11 N1 - C6 - O6 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA B 12 O5' - C5' - C4' ANGL. DEV. = -8.6 DEGREES REMARK 500 DA B 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA B 12 C3' - O3' - P ANGL. DEV. = 15.8 DEGREES REMARK 500 DG B 13 N1 - C6 - O6 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 14 O5' - C5' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 DG B 15 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 15 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 16 O5' - C5' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 17 O4' - C4' - C3' ANGL. DEV. = -2.8 DEGREES REMARK 500 DG B 17 O4' - C1' - N9 ANGL. DEV. = -6.1 DEGREES REMARK 500 DG B 17 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DA B 18 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DA B 18 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES REMARK 500 DA B 18 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 DG B 19 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DG B 20 O5' - C5' - C4' ANGL. DEV. = -5.2 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 CPT A 101 PT1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG A 5 N7 REMARK 620 2 CPT A 101 N1 90.8 REMARK 620 3 CPT A 101 N2 179.7 89.0 REMARK 620 4 DG B 15 N7 86.8 177.6 93.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CPT A 101 DBREF 1A2E A 1 10 PDB 1A2E 1A2E 1 10 DBREF 1A2E B 11 20 PDB 1A2E 1A2E 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 101 3 HETNAM CPT CISPLATIN HETSYN CPT DIAMMINE(DICHLORO)PLATINUM FORMUL 3 CPT CL2 H6 N2 PT FORMUL 4 HOH *92(H2 O) LINK N7 DG A 5 PT1 CPT A 101 1555 1555 2.00 LINK PT1 CPT A 101 N7 DG B 15 1555 1555 2.00 SITE 1 AC1 8 DG A 5 DT A 7 DC A 8 HOH A 106 SITE 2 AC1 8 HOH A 135 DG B 15 DG B 17 HOH B 25 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