Header list of 1jo1.pdb file
Complete list - 23 202 Bytes
HEADER DNA 26-JUL-01 1JO1
TITLE N7-GUANINE ADDUCT OF 2,7-DIAMINOMITOSENE WITH DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*TP*GP*(DAJ)GP*TP*AP*TP*AP*CP*CP*AP*C)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: SYNTHESIZED USING ABI-380B SYNTHESIZER
KEYWDS DOUBLE HELIX, MAJOR GROOVE BINDING DRUG, GUANINE-N7-ALKYLATOR, DNA
EXPDTA SOLUTION NMR
AUTHOR G.SUBRAMANIAM,M.M.PAZ,G.S.KUMAR,A.DAS,Y.PALOM,C.C.CLEMENT,D.J.PATEL,
AUTHOR 2 M.TOMASZ
REVDAT 4 23-FEB-22 1JO1 1 REMARK LINK
REVDAT 3 24-FEB-09 1JO1 1 VERSN
REVDAT 2 01-APR-03 1JO1 1 JRNL
REVDAT 1 12-SEP-01 1JO1 0
JRNL AUTH G.SUBRAMANIAM,M.M.PAZ,G.SURESH KUMAR,A.DAS,Y.PALOM,
JRNL AUTH 2 C.C.CLEMENT,D.J.PATEL,M.TOMASZ
JRNL TITL SOLUTION STRUCTURE OF A GUANINE-N7-LINKED COMPLEX OF THE
JRNL TITL 2 MITOMYCIN C METABOLITE 2,7-DIAMINOMITOSENE AND DNA. BASIS OF
JRNL TITL 3 SEQUENCE SELECTIVITY.
JRNL REF BIOCHEMISTRY V. 40 10473 2001
JRNL REFN ISSN 0006-2960
JRNL PMID 11523988
JRNL DOI 10.1021/BI010965A
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1, X-PLOR 3.01
REMARK 3 AUTHORS : VARIAN INSTRUMENTS (VNMR), A. BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON 126
REMARK 3 INTRAMOLECULAR DNA CONSTRAINTS, 30 H-BONDING CONSTRAINTS, 48
REMARK 3 INTERMOLECULAR DRUG-DNA CONSTRAINTS, AND 48 DIHEDRAL CONSTRAINTS
REMARK 4
REMARK 4 1JO1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUL-01.
REMARK 100 THE DEPOSITION ID IS D_1000013991.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 303
REMARK 210 PH : 6.8; 6.8
REMARK 210 IONIC STRENGTH : 0.1 M NACL; 0.1 M NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.2 MM D(GTG(+G)TATACCAC) DUPLEX
REMARK 210 IN 0.01 M SODIUM PHOSPHATE, 0.1
REMARK 210 M NACL, 0.001M EDTA; 1.2 MM
REMARK 210 D(GTG(+G)TATACCAC) DUPLEX IN
REMARK 210 0.01 M SODIUM PHOSPHATE, 0.1 M
REMARK 210 NACL, 0.001M EDTA
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; P-COSY; HOHAHA
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITYPLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : FELIX 3.0, X-PLOR 3.01
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND MOLECULAR
REMARK 210 DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 12
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST NUMBER OF NOE VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D-NOE
REMARK 210 BUILDUP STUDIES IN H2O AND D2O BUFFERS.
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 O4 DT B 7 HN1 DAJ A 13 1.48
REMARK 500 O4 DT A 7 HN1 DAJ B 13 1.48
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 DT A 2 C5 DT A 2 C7 0.041
REMARK 500 DG A 4 N7 DG A 4 C8 0.068
REMARK 500 DT A 5 C5 DT A 5 C7 0.051
REMARK 500 DT A 7 C5 DT A 7 C7 0.038
REMARK 500 DT B 2 C5 DT B 2 C7 0.041
REMARK 500 DG B 4 N7 DG B 4 C8 0.068
REMARK 500 DT B 5 C5 DT B 5 C7 0.051
REMARK 500 DT B 7 C5 DT B 7 C7 0.037
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 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT A 2 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES
REMARK 500 DG A 4 C4' - C3' - C2' ANGL. DEV. = -4.7 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DG A 4 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES
REMARK 500 DT A 5 C4 - C5 - C7 ANGL. DEV. = 5.5 DEGREES
REMARK 500 DT A 5 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES
REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES
REMARK 500 DC A 9 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 DC A 9 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DC A 10 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DC A 12 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 1 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 DG B 1 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DT B 2 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DG B 3 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES
REMARK 500 DG B 4 C4' - C3' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 DG B 4 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DG B 4 N9 - C4 - C5 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT B 5 C4 - C5 - C7 ANGL. DEV. = 5.6 DEGREES
REMARK 500 DT B 5 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES
REMARK 500 DA B 6 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES
REMARK 500 DT B 7 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 DC B 9 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES
REMARK 500 DC B 9 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 DC B 9 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 DC B 10 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.4 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 DAJ A 13
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAJ B 13
DBREF 1JO1 A 1 12 PDB 1JO1 1JO1 1 12
DBREF 1JO1 B 1 12 PDB 1JO1 1JO1 1 12
SEQRES 1 A 12 DG DT DG DG DT DA DT DA DC DC DA DC
SEQRES 1 B 12 DG DT DG DG DT DA DT DA DC DC DA DC
HET DAJ A 13 33
HET DAJ B 13 33
HETNAM DAJ DECARBAMOYL-2,7-DIAMINOMITOSENE
FORMUL 3 DAJ 2(C13 H16 N3 O2 1+)
LINK N7 DG A 4 C10 DAJ A 13 1555 1555 1.50
LINK N7 DG B 4 C10 DAJ B 13 1555 1555 1.50
SITE 1 AC1 6 DG A 3 DG A 4 DT A 5 DA A 6
SITE 2 AC1 6 DA B 6 DT B 7
SITE 1 AC2 6 DA A 6 DT A 7 DG B 3 DG B 4
SITE 2 AC2 6 DT B 5 DA B 6
CRYST1 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 - 23 202 Bytes