Header list of 1jdg.pdb file
Complete list - 23 202 Bytes
HEADER DNA 13-JUN-01 1JDG TITLE SOLUTION STRUCTURE OF A TRANS-OPENED (10S)-DA ADDUCT OF (+)-(7S,8R,9S, TITLE 2 10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9,10-TETRAHYDROBENZO[A]PYRENE IN A TITLE 3 FULLY COMPLEMENTARY DNA DUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*GP*TP*CP*(BPA)AP*CP*GP*AP*GP*G)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS SYN GLYCOSIDIC TORSION ANGLE, BENZO[A]PYRENE DIOL EPOXIDE, DA ADDUCT, KEYWDS 2 DNA EXPDTA SOLUTION NMR AUTHOR P.PRADHAN,S.TIRUMALA,X.LIU,J.M.SAYER,D.M.JERINA,H.J.C.YEH REVDAT 4 23-FEB-22 1JDG 1 REMARK LINK REVDAT 3 24-FEB-09 1JDG 1 VERSN REVDAT 2 01-APR-03 1JDG 1 JRNL REVDAT 1 04-JUL-01 1JDG 0 JRNL AUTH P.PRADHAN,S.TIRUMALA,X.LIU,J.M.SAYER,D.M.JERINA,H.J.YEH JRNL TITL SOLUTION STRUCTURE OF A TRANS-OPENED (10S)-DA ADDUCT OF JRNL TITL 2 (+)-(7S,8R,9S,10R)-7,8-DIHYDROXY-9,10-EPOXY-7,8,9, JRNL TITL 3 10-TETRAHYDROBENZO[A]PYRENE IN A FULLY COMPLEMENTARY DNA JRNL TITL 4 DUPLEX: EVIDENCE FOR A MAJOR SYN CONFORMATION. JRNL REF BIOCHEMISTRY V. 40 5870 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11352722 JRNL DOI 10.1021/BI002896Q REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 3.0 REMARK 3 AUTHORS : WEINER, S. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1JDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013650. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.1M REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 2MM DNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : VXRS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, IRMA 2000, INSIGHT REMARK 210 II REMARK 210 METHOD USED : SIMULATED ANNEALING, RESTRAINT REMARK 210 MOLECULAR DYNAMICS, RELAXATION REMARK 210 MATRIX ANALYSIS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 11 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: 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' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC A 7 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 9 O4' - C1' - N9 ANGL. DEV. = 3.3 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 1B O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC B 2B O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT B 3B O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 4B O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 5B O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DT B 6B O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 7B O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 8B O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 9B O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 10B O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DG B 11B O4' - C1' - N9 ANGL. DEV. = 2.8 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 3 0.08 SIDE CHAIN REMARK 500 DT A 4 0.09 SIDE CHAIN REMARK 500 DC A 5 0.08 SIDE CHAIN REMARK 500 DT B 3B 0.07 SIDE CHAIN REMARK 500 DG B 11B 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 BPA A 12 DBREF 1JDG A 1 11 PDB 1JDG 1JDG 1 11 DBREF 1JDG B 1B 11B PDB 1JDG 1JDG 1 11 SEQRES 1 A 11 DC DG DG DT DC DA DC DG DA DG DG SEQRES 1 B 11 DC DC DT DC DG DT DG DA DC DC DG HET BPA A 12 38 HETNAM BPA 7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE FORMUL 3 BPA C20 H16 O3 LINK N6 DA A 6 C10 BPA A 12 1555 1555 1.48 SITE 1 AC1 4 DA A 6 DC A 7 DG B 5B DT B 6B 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 - 23 202 Bytes