HEADER DNA 22-SEP-94 264D TITLE THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA DODECAMER TITLE 2 D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR-GROOVE-BINDING DRUG HOECHST TITLE 3 33258 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, DNA EXPDTA X-RAY DIFFRACTION AUTHOR M.C.VEGA,I.GARCIA-SAEZ,J.AYMAMI,R.ERITJA,G.A.VAN DER MAREL,J.H.VAN AUTHOR 2 BOOM,A.RICH,M.COLL REVDAT 5 14-FEB-24 264D 1 REMARK REVDAT 4 14-DEC-16 264D 1 REMARK VERSN REVDAT 3 24-FEB-09 264D 1 VERSN REVDAT 2 01-APR-03 264D 1 JRNL REVDAT 1 31-MAR-95 264D 0 JRNL AUTH M.C.VEGA,I.GARCIA SAEZ,J.AYMAMI,R.ERITJA,G.A.VAN DER MAREL, JRNL AUTH 2 J.H.VAN BOOM,A.RICH,M.COLL JRNL TITL THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA JRNL TITL 2 DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE JRNL TITL 3 MINOR-GROOVE-BINDING DRUG HOECHST 33258. JRNL REF EUR.J.BIOCHEM. V. 222 721 1994 JRNL REFN ISSN 0014-2956 JRNL PMID 7517864 JRNL DOI 10.1111/J.1432-1033.1994.TB18917.X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.CARRONDO,M.COLL,J.AYMAMI,A.H.WANG,G.A.VAN DER MAREL, REMARK 1 AUTH 2 J.H.VAN BOOM,A.RICH REMARK 1 TITL BINDING OF A HOECHST DYE TO D(CGCGATATCGCG) AND ITS REMARK 1 TITL 2 INFLUENCE ON THE CONFORMATION OF THE DNA FRAGMENT. REMARK 1 REF BIOCHEMISTRY V. 28 7849 1989 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 2482071 REMARK 1 REFERENCE 2 REMARK 1 AUTH M.COLL,C.A.FREDERICK,A.H.-J.WANG,A.RICH REMARK 1 TITL A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE REMARK 1 TITL 2 PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX REMARK 1 TITL 3 WITH DISTAMYCIN REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 84 8385 1987 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.5 REMARK 3 NUMBER OF REFLECTIONS : 2253 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL 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 : 32 REMARK 3 SOLVENT ATOMS : 18 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 3.710 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 264D 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_1000177676. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ELLIOTT GX-21 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2291 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.440 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.00, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 12.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.65000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.65000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.70000 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 DC A 1 O5' REMARK 480 DC B 13 O5' 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' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 DC A 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA A 5 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = -8.2 DEGREES REMARK 500 DT A 7 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.0 DEGREES REMARK 500 DT A 9 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 DG A 10 C5' - C4' - C3' ANGL. DEV. = -14.0 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 13 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA B 18 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 DT B 19 C1' - O4' - C4' ANGL. DEV. = -8.3 DEGREES REMARK 500 DT B 19 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 DT B 20 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DT B 21 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 23 C4' - C3' - C2' ANGL. DEV. = -5.2 DEGREES REMARK 500 DC B 23 O4' - C1' - N1 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 23 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DG A 2 0.08 SIDE CHAIN REMARK 500 DC A 3 0.13 SIDE CHAIN REMARK 500 DG A 10 0.10 SIDE CHAIN REMARK 500 DC A 11 0.09 SIDE CHAIN REMARK 500 DC B 13 0.07 SIDE CHAIN REMARK 500 DG B 14 0.08 SIDE CHAIN REMARK 500 DC B 15 0.07 SIDE CHAIN REMARK 500 DT B 21 0.06 SIDE CHAIN REMARK 500 DC B 23 0.18 SIDE CHAIN 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 HT B 25 DBREF 264D A 1 12 PDB 264D 264D 1 12 DBREF 264D B 13 24 PDB 264D 264D 13 24 SEQRES 1 A 12 DC DG DC DA DA DA DT DT DT DG DC DG SEQRES 1 B 12 DC DG DC DA DA DA DT DT DT DG DC DG HET HT B 25 32 HETNAM HT 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'- HETNAM 2 HT BI-BENZIMIDAZOLE HETSYN HT HOECHST 33258 FORMUL 3 HT C25 H24 N6 O FORMUL 4 HOH *18(H2 O) SITE 1 AC1 12 DA A 6 DT A 7 DT A 8 DT A 9 SITE 2 AC1 12 DG A 10 DC A 11 DA B 17 DA B 18 SITE 3 AC1 12 DT B 19 DT B 20 DT B 21 DG B 24 CRYST1 25.500 41.400 65.300 90.00 90.00 90.00 P 21 21 21 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 0.039216 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024155 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015314 0.00000