10 20 30 40 50 60 70 80 403D - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 10-JUN-98 403D
TITLE 5'-D(*CP*GP*CP*(HYD)AP*AP*AP*TP*TP*TP*GP*CP*G)-3', 2'-(4- TITLE 2 ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI- TITLE 3 BENZIMIDAZOLE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*CP*(IGU) COMPND 3 P*AP*AP*TP*TP*TP*GP*CP*G)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES
KEYWDS DNA/DRUG COMPLEX, B-DNA DOUBLE HELIX
EXPDTA X-RAY DIFFRACTION
AUTHOR H.ROBINSON,Y.-G.GAO,C.BAUER,C.ROBERTS,C.SWITZER,A.H.-J.WANG
REVDAT 3 24-FEB-09 403D 1 VERSN REVDAT 2 01-APR-03 403D 1 JRNL REVDAT 1 06-JUL-98 403D 0
JRNL AUTH H.ROBINSON,Y.G.GAO,C.BAUER,C.ROBERTS,C.SWITZER, JRNL AUTH 2 A.H.WANG JRNL TITL 2'-DEOXYISOGUANOSINE ADOPTS MORE THAN ONE TAUTOMER JRNL TITL 2 TO FORM BASE PAIRS WITH THYMIDINE OBSERVED BY JRNL TITL 3 HIGH-RESOLUTION CRYSTAL STRUCTURE ANALYSIS. JRNL REF BIOCHEMISTRY V. 37 10897 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9692982 JRNL DOI 10.1021/BI980818L
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 3 CROSS-VALIDATION METHOD : R-FREE 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) : 0.245 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.242 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 564 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 11253 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.219 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.216 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.296 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 446 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 8608 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 : 43 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.031 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL 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 403D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-97 REMARK 200 TEMPERATURE (KELVIN) : 123.00 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M 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 : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : BIOTEX REMARK 200 DATA SCALING SOFTWARE : BIOTEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11253 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH 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 (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.50, VAPOR DIFFUSION
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 12.87950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.15350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.54200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.15350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 12.87950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.54200 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 DG A 2 C6 DG A 2 O6 0.096 REMARK 500 DG A 10 C6 DG A 10 O6 0.094 REMARK 500 DG A 12 C6 DG A 12 O6 0.089 REMARK 500 DG B 14 C6 DG B 14 O6 0.082 REMARK 500 DG B 22 C6 DG B 22 O6 0.094 REMARK 500 DG B 24 C6 DG B 24 O6 0.079 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 DG A 2 O4' - C1' - N9 ANGL. DEV. = -7.0 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 DA A 6 O5' - C5' - C4' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 7 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DC A 11 O4' - C4' - C3' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG A 12 N3 - C2 - N2 ANGL. DEV. = 4.5 DEGREES REMARK 500 DC B 13 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 DC B 13 C3' - O3' - P ANGL. DEV. = -7.9 DEGREES REMARK 500 DC B 15 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG B 24 O4' - C1' - C2' ANGL. DEV. = 3.9 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 DC A 3 0.06 SIDE_CHAIN REMARK 500 DA A 5 0.05 SIDE_CHAIN REMARK 500 DT A 7 0.07 SIDE_CHAIN REMARK 500 DC A 11 0.12 SIDE_CHAIN REMARK 500 DG B 14 0.06 SIDE_CHAIN REMARK 500 DA B 17 0.06 SIDE_CHAIN REMARK 500 DT B 21 0.08 SIDE_CHAIN REMARK 500 DC B 23 0.10 SIDE_CHAIN 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 MG A 26 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B1142 O REMARK 620 2 HOH B1138 O 89.2 REMARK 620 3 HOH B1143 O 89.8 89.6 REMARK 620 4 HOH A1139 O 87.2 176.3 89.6 REMARK 620 5 HOH A1141 O 90.9 90.1 179.2 90.8 REMARK 620 6 HOH A1140 O 179.1 91.7 90.5 91.9 88.8 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HT1 A 25 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 26
DBREF 403D A 1 12 PDB 403D 403D 1 12 DBREF 403D B 13 24 PDB 403D 403D 13 24
SEQRES 1 A 12 DC DG DC IGU DA DA DT DT DT DG DC DG SEQRES 1 B 12 DC DG DC IGU DA DA DT DT DT DG DC DG
MODRES 403D IGU A 4 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE MODRES 403D IGU B 16 DG 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE
HET IGU A 4 22 HET IGU B 16 22 HET HT1 A 25 34 HET MG A 26 1
HETNAM IGU 2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE HETNAM HT1 2'-(4-ETHOXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'- HETNAM 2 HT1 BI-BENZIMIDAZOLE HETNAM MG MAGNESIUM ION
HETSYN HT1 HOECHST 33342
FORMUL 1 IGU 2(C10 H14 N5 O7 P) FORMUL 3 HT1 C27 H28 N6 O FORMUL 4 MG MG 2+ FORMUL 5 HOH *128(H2 O)
LINK MG MG A 26 O HOH B1142 1555 1555 2.09 LINK MG MG A 26 O HOH B1138 1555 1555 2.06 LINK MG MG A 26 O HOH B1143 1555 1555 2.05 LINK MG MG A 26 O HOH A1139 1555 1555 2.05 LINK MG MG A 26 O HOH A1141 1555 1555 2.06 LINK MG MG A 26 O HOH A1140 1555 1555 2.04 LINK O3' DC A 3 P IGU A 4 1555 1555 1.59 LINK O3' IGU A 4 P DA A 5 1555 1555 1.60 LINK O3' DC B 15 P IGU B 16 1555 1555 1.60 LINK O3' IGU B 16 P DA B 17 1555 1555 1.61
SITE 1 AC1 15 IGU A 4 DA A 5 DA A 6 DT A 7 SITE 2 AC1 15 DT A 8 DT A 9 DG A 12 HOH A1035 SITE 3 AC1 15 HOH A1072 HOH A1093 DA B 18 DT B 19 SITE 4 AC1 15 DT B 20 DT B 21 HOH B1101 SITE 1 AC2 6 HOH A1139 HOH A1140 HOH A1141 HOH B1138 SITE 2 AC2 6 HOH B1142 HOH B1143
CRYST1 25.759 41.084 64.307 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 0.038821 0.000000 0.000000 0.00000
SCALE2 0.000000 0.024340 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015550 0.00000