HEADER DNA 21-MAY-02 1LU5
TITLE 2.4 ANGSTROM CRYSTAL STRUCTURE OF THE ASYMMETRIC PLATINUM COMPLEX
TITLE 2 {PT(AMMINE)(CYCLOHEXYLAMINE)}2+ BOUND TO A DODECAMER DNA 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, C;
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, D;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES
KEYWDS PLATINUM-DNA COMPLEX, DNA
EXPDTA X-RAY DIFFRACTION
AUTHOR A.P.SILVERMAN,W.BU,S.M.COHEN,S.J.LIPPARD
REVDAT 4 14-FEB-24 1LU5 1 REMARK
REVDAT 3 08-FEB-12 1LU5 1 REMARK VERSN
REVDAT 2 24-FEB-09 1LU5 1 VERSN
REVDAT 1 20-DEC-02 1LU5 0
JRNL AUTH A.P.SILVERMAN,W.BU,S.M.COHEN,S.J.LIPPARD
JRNL TITL 2.4-A CRYSTAL STRUCTURE OF THE ASYMMETRIC PLATINUM COMPLEX
JRNL TITL 2 {PT(AMMINE)(CYCLOHEXYLAMINE)}2+ BOUND TO A DODECAMER DNA
JRNL TITL 3 DUPLEX
JRNL REF J.BIOL.CHEM. V. 277 49743 2002
JRNL REFN ISSN 0021-9258
JRNL PMID 12377787
JRNL DOI 10.1074/JBC.M206979200
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) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
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) : 0.235
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.294
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 733
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6604
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.235
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.201
REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.250
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 565
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5267
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 0
REMARK 3 NUCLEIC ACID ATOMS : 972
REMARK 3 HETEROGEN ATOMS : 18
REMARK 3 SOLVENT ATOMS : 47
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1037.0
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4163
REMARK 3 NUMBER OF RESTRAINTS : 4897
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.005
REMARK 3 ANGLE DISTANCES (A) : 0.022
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.000
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.004
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.005
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.075
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: NULL
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1LU5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUN-02.
REMARK 100 THE DEPOSITION ID IS D_1000016271.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-AUG-01
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7337
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.08200
REMARK 200 R SYM (I) : 0.09000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.2000
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) : 2.49
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.25100
REMARK 200 R SYM FOR SHELL (I) : 0.27700
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: SHELXS
REMARK 200 STARTING MODEL: PDB ENTRY 1AIO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 67.40
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.78
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SPERMINE, SODIUM CACODYLATE, MAGNESIUM
REMARK 280 ACETATE, PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D
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 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DG B 23 O4' - C1' - N9 ANGL. DEV. = 2.1 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 LPT A 49 PT
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG A 6 N7
REMARK 620 2 LPT A 49 N2 159.5
REMARK 620 3 LPT A 49 N1 96.4 87.6
REMARK 620 4 DG A 7 N7 92.3 87.5 167.2
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 LPT C 50 PT
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 DG C 30 N7
REMARK 620 2 LPT C 50 N2 167.6
REMARK 620 3 LPT C 50 N1 73.6 99.1
REMARK 620 4 DG C 31 N7 98.5 88.2 171.7
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 LPT A 49
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LPT C 50
DBREF 1LU5 A 1 12 PDB 1LU5 1LU5 1 12
DBREF 1LU5 B 13 24 PDB 1LU5 1LU5 13 24
DBREF 1LU5 C 25 36 PDB 1LU5 1LU5 25 36
DBREF 1LU5 D 37 48 PDB 1LU5 1LU5 37 48
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
SEQRES 1 C 12 DC DC DT DC DT DG DG DT DC DT DC DC
SEQRES 1 D 12 DG DG DA DG DA DC DC DA DG DA DG DG
HET LPT A 49 9
HET LPT C 50 9
HETNAM LPT CIS-(AMMINE)(CYCLOHEXYLAMINE)PLATINUM(II) COMPLEX
FORMUL 5 LPT 2(C6 H16 N2 PT 2+)
FORMUL 7 HOH *47(H2 O)
LINK N7 DG A 6 PT LPT A 49 1555 1555 1.97
LINK N7 DG A 7 PT LPT A 49 1555 1555 1.96
LINK N7 DG C 30 PT LPT C 50 1555 1555 1.96
LINK N7 DG C 31 PT LPT C 50 1555 1555 1.96
SITE 1 AC1 5 DG A 6 DG A 7 DT A 8 HOH A 204
SITE 2 AC1 5 HOH A 222
SITE 1 AC2 4 DT C 29 DG C 30 DG C 31 DT C 32
CRYST1 31.644 35.638 46.556 79.53 83.02 81.36 P 1 2
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 0.031602 -0.004802 -0.003113 0.00000
SCALE2 0.000000 0.028382 -0.004795 0.00000
SCALE3 0.000000 0.000000 0.021947 0.00000