Header list of 226d.pdb file
Complete list - 9 202 Bytes
HEADER DNA 19-JUL-95 226D TITLE SOLUTION CONFORMATION OF A BIZELESIN A-TRACT DUPLEX ADDUCT, NMR, 1 TITLE 2 STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*AP*CP*G)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*GP*TP*AP*AP*AP*AP*AP*CP*G)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, DNA-LIGAND, ADDUCT, BIZELESIN EXPDTA SOLUTION NMR AUTHOR A.S.THOMPSON,L.H.HURLEY REVDAT 4 09-MAR-22 226D 1 REMARK REVDAT 3 24-FEB-09 226D 1 VERSN REVDAT 2 01-APR-03 226D 1 JRNL REVDAT 1 29-JAN-96 226D 0 JRNL AUTH A.S.THOMPSON,L.H.HURLEY JRNL TITL SOLUTION CONFORMATION OF A BIZELESIN A-TRACT DUPLEX ADDUCT: JRNL TITL 2 DNA-DNA CROSS-LINKING OF AN A-TRACT STRAIGHTENS OUT BENT JRNL TITL 3 DNA. JRNL REF J.MOL.BIOL. V. 252 86 1995 JRNL REFN ISSN 0022-2836 JRNL PMID 7666436 JRNL DOI 10.1006/JMBI.1994.0477 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS REFINED USING A REMARK 3 COMBINATION OF RESTRAINED MOLECULAR MECHANICS AND DYNAMICS USING REMARK 3 THE AMBER 4.0 PROGRAM (UCSF). DISTANCE RESTRAINTS WERE REMARK 3 CALCULATED USING MARDIGRAS FROM NUCLEAR OVERHAUSER EFFECT REMARK 3 SPECTRA AT VARIOUS MIXING TIMES. REMARK 4 REMARK 4 226D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177602. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : RESTRAINED MOLECULAR MECHANICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: CLOSE CONTACTS 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 N3 DA B 18 CI' BIZ B 21 1.46 REMARK 500 N3 DA A 8 C18 BIZ B 21 1.46 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 DC A 1 O5' DC A 1 C5' -0.495 REMARK 500 DC A 1 C5' DC A 1 C4' -0.171 REMARK 500 DC A 1 C4' DC A 1 C3' -0.119 REMARK 500 DC A 1 C3' DC A 1 C2' -0.070 REMARK 500 DC A 1 C2' DC A 1 C1' -0.103 REMARK 500 DC A 1 O4' DC A 1 C1' -0.093 REMARK 500 DC A 1 O4' DC A 1 C4' -0.160 REMARK 500 DC A 1 O3' DC A 1 C3' -0.125 REMARK 500 DC A 1 C2 DC A 1 O2 -0.071 REMARK 500 DC A 1 N1 DC A 1 C2 -0.075 REMARK 500 DC A 1 N1 DC A 1 C6 -0.071 REMARK 500 DC A 1 N3 DC A 1 C4 -0.064 REMARK 500 DC A 1 C4 DC A 1 C5 -0.061 REMARK 500 DC A 1 O3' DG A 2 P -0.137 REMARK 500 DG A 2 P DG A 2 OP1 -0.212 REMARK 500 DG A 2 P DG A 2 OP2 -0.241 REMARK 500 DG A 2 P DG A 2 O5' -0.106 REMARK 500 DG A 2 O5' DG A 2 C5' -0.160 REMARK 500 DG A 2 C5' DG A 2 C4' -0.087 REMARK 500 DG A 2 O4' DG A 2 C4' -0.090 REMARK 500 DG A 2 O3' DG A 2 C3' -0.053 REMARK 500 DT A 3 C3' DT A 3 C2' -0.054 REMARK 500 DT A 3 O4' DT A 3 C4' -0.063 REMARK 500 DT A 3 O3' DT A 3 C3' -0.052 REMARK 500 DT A 4 C3' DT A 4 C2' -0.084 REMARK 500 DT A 4 O4' DT A 4 C4' -0.078 REMARK 500 DT A 4 O3' DT A 4 C3' -0.099 REMARK 500 DT A 5 P DT A 5 OP1 -0.109 REMARK 500 DT A 5 P DT A 5 OP2 -0.111 REMARK 500 DT A 5 O4' DT A 5 C4' -0.069 REMARK 500 DT A 7 O4' DT A 7 C4' -0.062 REMARK 500 DA A 8 O3' DA A 8 C3' -0.037 REMARK 500 DA A 8 C2 DA A 8 N3 0.160 REMARK 500 DA A 8 O3' DC A 9 P -0.131 REMARK 500 DC A 9 P DC A 9 OP1 -0.137 REMARK 500 DC A 9 O4' DC A 9 C4' -0.065 REMARK 500 DG A 10 O4' DG A 10 C4' -0.066 REMARK 500 DG A 10 O3' DG A 10 C3' -0.070 REMARK 500 DC B 11 O5' DC B 11 C5' -0.434 REMARK 500 DC B 11 C5' DC B 11 C4' -0.072 REMARK 500 DC B 11 O4' DC B 11 C4' -0.111 REMARK 500 DC B 11 O3' DC B 11 C3' -0.059 REMARK 500 DC B 11 N1 DC B 11 C2 -0.062 REMARK 500 DC B 11 N1 DC B 11 C6 -0.048 REMARK 500 DG B 12 O4' DG B 12 C4' -0.073 REMARK 500 DG B 12 O3' DG B 12 C3' -0.036 REMARK 500 DT B 13 O3' DT B 13 C3' -0.044 REMARK 500 DA B 14 O3' DA B 14 C3' -0.051 REMARK 500 DA B 15 P DA B 15 OP1 -0.142 REMARK 500 DA B 15 P DA B 15 OP2 -0.127 REMARK 500 REMARK 500 THIS ENTRY HAS 68 BOND DEVIATIONS. 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 O5' - C5' - C4' ANGL. DEV. = 21.6 DEGREES REMARK 500 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT A 3 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DA A 8 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 12.2 DEGREES REMARK 500 DA A 8 N1 - C2 - N3 ANGL. DEV. = -5.8 DEGREES REMARK 500 DA A 8 C2 - N3 - C4 ANGL. DEV. = 4.9 DEGREES REMARK 500 DA A 8 N3 - C4 - C5 ANGL. DEV. = -8.4 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = 6.2 DEGREES REMARK 500 DA A 8 N3 - C4 - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA A 8 C3' - O3' - P ANGL. DEV. = 9.4 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA B 14 O4' - C1' - C2' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA B 14 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DA B 15 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 DA B 16 O4' - C1' - C2' ANGL. DEV. = -6.1 DEGREES REMARK 500 DA B 16 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 DA B 16 C3' - O3' - P ANGL. DEV. = 14.0 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DA B 18 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 18 N1 - C2 - N3 ANGL. DEV. = -6.3 DEGREES REMARK 500 DA B 18 C2 - N3 - C4 ANGL. DEV. = 5.9 DEGREES REMARK 500 DA B 18 N3 - C4 - C5 ANGL. DEV. = -9.1 DEGREES REMARK 500 DA B 18 C4 - C5 - C6 ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 18 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA B 18 N3 - C4 - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 DA B 18 C6 - C5 - N7 ANGL. DEV. = -4.3 DEGREES REMARK 500 DC B 19 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DG B 20 C4' - C3' - C2' ANGL. DEV. = 7.9 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 DT A 4 0.06 SIDE CHAIN REMARK 500 DT A 6 0.07 SIDE CHAIN REMARK 500 DA A 8 0.08 SIDE CHAIN REMARK 500 DC A 9 0.10 SIDE CHAIN REMARK 500 DG A 10 0.07 SIDE CHAIN REMARK 500 DA B 18 0.06 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 BIZ B 21 DBREF 226D A 1 10 PDB 226D 226D 1 10 DBREF 226D B 11 20 PDB 226D 226D 11 20 SEQRES 1 A 10 DC DG DT DT DT DT DT DA DC DG SEQRES 1 B 10 DC DG DT DA DA DA DA DA DC DG HET BIZ B 21 56 HETNAM BIZ BIZELESIN FORMUL 3 BIZ C43 H38 N8 O5 SITE 1 AC1 10 DT A 4 DT A 7 DA A 8 DC A 9 SITE 2 AC1 10 DT B 13 DA B 14 DA B 16 DA B 17 SITE 3 AC1 10 DA B 18 DC B 19 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000
Complete list - 9 202 Bytes