HEADER DNA 28-NOV-06 2O1I TITLE RH(BPY)2CHRYSI COMPLEXED TO MISMATCHED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS KEYWDS DNA MISMATCH, METALLOINTERCALATOR, DNA RECOGNITION, DNA EXPDTA X-RAY DIFFRACTION AUTHOR V.C.PIERRE,J.T.KAISER,J.K.BARTON REVDAT 4 27-DEC-23 2O1I 1 REMARK REVDAT 3 24-FEB-09 2O1I 1 VERSN REVDAT 2 23-JAN-07 2O1I 1 JRNL REVDAT 1 09-JAN-07 2O1I 0 JRNL AUTH V.C.PIERRE,J.T.KAISER,J.K.BARTON JRNL TITL INSIGHTS INTO FINDING A MISMATCH THROUGH THE STRUCTURE OF A JRNL TITL 2 MISPAIRED DNA BOUND BY A RHODIUM INTERCALATOR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 429 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17194756 JRNL DOI 10.1073/PNAS.0610170104 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 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) : 0.152 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.130 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 12124 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 242 REMARK 3 HETEROGEN ATOMS : 135 REMARK 3 SOLVENT ATOMS : 75 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 384.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 178.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4070 REMARK 3 NUMBER OF RESTRAINTS : 5578 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.024 REMARK 3 ANGLE DISTANCES (A) : 0.041 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.014 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.000 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.022 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.036 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.109 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 2O1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-06; 19-MAY-06 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; SSRL REMARK 200 BEAMLINE : NULL; BL11-1 REMARK 200 X-RAY GENERATOR MODEL : RIGAKU; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.03317 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; ADSC QUANTUM REMARK 200 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17269 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 24.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.01500 REMARK 200 R SYM FOR SHELL (I) : 1.50000 REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SRCL2 40MM, MGCL2 10MM, NA-CACODYLATE REMARK 280 20MM, SPERMINE-4HCL 6MM, MPD 5%(V/V)EQUILIBRATED AGAINST 35% MPD, REMARK 280 PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 28.78000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.37000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.37000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.17000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.37000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.37000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.39000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.37000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.37000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.17000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.37000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.37000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.39000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 28.78000 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 SECOND PART OF THE BIOLOGICAL ASSEMBLY IS GENERATED BY REMARK 300 THE TWO FOLD AXIS Y,X,-Z. 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2013 LIES ON A SPECIAL POSITION. 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 O5' DC A 10 O HOH A 2078 1.26 REMARK 500 P DC A 10 O HOH A 2078 1.41 REMARK 500 O HOH A 2059 O HOH A 2069 1.54 REMARK 500 OP1 DC A 10 O HOH A 2078 1.55 REMARK 500 O HOH A 2034 O HOH A 2073 1.59 REMARK 500 O HOH A 2036 O HOH A 2074 2.04 REMARK 500 O HOH A 2061 O HOH A 2085 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 DG A 2 C5 DG A 2 N7 0.041 REMARK 500 DG A 12 O4' DG A 12 C1' 0.126 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 DA A 4 O4' - C4' - C3' ANGL. DEV. = -2.7 DEGREES REMARK 500 DA A 4 O4' - C1' - N9 ANGL. DEV. = -7.8 DEGREES REMARK 500 DA A 5 C3' - C2' - C1' ANGL. DEV. = -6.0 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA A 6 C2 - N3 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 DT A 7 O4' - C4' - C3' ANGL. DEV. = -4.7 DEGREES REMARK 500 DT A 7 C4' - C3' - C2' ANGL. DEV. = 7.0 DEGREES REMARK 500 DT A 7 N1 - C1' - C2' ANGL. DEV. = 8.5 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = -8.6 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 8 C6 - N1 - C2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC A 9 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC A 9 N3 - C4 - C5 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC A 9 C5 - C4 - N4 ANGL. DEV. = -6.0 DEGREES REMARK 500 DC A 10 O5' - C5' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DG A 12 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 DG A 12 N9 - C1' - C2' ANGL. DEV. = 10.1 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = -14.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R1C A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R1C A 2011 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE R1C A 1002 DBREF 2O1I A 1 12 PDB 2O1I 2O1I 1 12 SEQRES 1 A 12 DC DG DG DA DA DA DT DT DC DC DC DG HET R1C A1001 45 HET R1C A2011 45 HET R1C A1002 45 HETNAM R1C BIS(2,2'-BIPYRIDINE-KAPPA~2~N~1~,N~1'~)[CHRYSENE-5,6- HETNAM 2 R1C DIIMINATO(2-)-KAPPA~2~N,N']RHODIUM(4+) HETSYN R1C DELTA-RHODIUM(III)- BIS-(2,2'-BIPYRIDYL)-5,6- HETSYN 2 R1C CHRYSENEQUINONE DIIMINE FORMUL 2 R1C 3(C38 H26 N6 RH 4+) FORMUL 5 HOH *75(H2 O) SITE 1 AC1 6 DC A 1 DA A 5 DA A 6 DT A 7 SITE 2 AC1 6 DG A 12 HOH A2047 SITE 1 AC2 7 DC A 1 DA A 5 DA A 6 DT A 7 SITE 2 AC2 7 DG A 12 HOH A2017 HOH A2047 SITE 1 AC3 8 DG A 3 DA A 4 DA A 5 DT A 8 SITE 2 AC3 8 DC A 9 DC A 10 DC A 11 HOH A2065 CRYST1 38.740 38.740 57.560 90.00 90.00 90.00 P 43 21 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 0.025813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025813 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017373 0.00000