Header list of 1fyy.pdb file
Complete list - 23 202 Bytes
HEADER DNA 03-OCT-00 1FYY TITLE HPRT GENE MUTATION HOTSPOT WITH A BPDE2(10R) ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HPRT DNA WITH BENZO[A]PYRENE-ADDUCTED DA7; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*TP*GP*CP*CP*CP*TP*TP*GP*AP*CP*TP*A)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE CONTAINS A MUTATIONAL HOTSPOT IN THE SOURCE 4 MOUSE HPRT GENE WITH A CHEMICALLY SYNTHESIZED BENZO[A]PYRENE ADDUCT; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES KEYWDS DNA LESIONS, BENZO[A]PYRENE, HPRT GENE, DIOL EPOXIDE ADDUCTS, SYN- KEYWDS 2 ANTI INTERCONVERSION, DNA EXPDTA SOLUTION NMR AUTHOR D.E.VOLK,J.S.RICE,B.A.LUXON,H.J.C.YEH,C.LIANG,G.XIE,J.M.SAYER, AUTHOR 2 D.M.JERINA,D.G.GORENSTEIN REVDAT 4 23-FEB-22 1FYY 1 REMARK LINK REVDAT 3 24-FEB-09 1FYY 1 VERSN REVDAT 2 01-APR-03 1FYY 1 JRNL REVDAT 1 06-DEC-00 1FYY 0 JRNL AUTH D.E.VOLK,J.S.RICE,B.A.LUXON,H.J.YEH,C.LIANG,G.XIE,J.M.SAYER, JRNL AUTH 2 D.M.JERINA,D.G.GORENSTEIN JRNL TITL NMR EVIDENCE FOR SYN-ANTI INTERCONVERSION OF A TRANS OPENED JRNL TITL 2 (10R)-DA ADDUCT OF BENZO[A]PYRENE (7S,8R)-DIOL JRNL TITL 3 (9R,10S)-EPOXIDE IN A DNA DUPLEX. JRNL REF BIOCHEMISTRY V. 39 14040 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11087351 JRNL DOI 10.1021/BI001669L REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5 REMARK 3 AUTHORS : CASE, D. A. ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FYY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012031. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 100 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM DUPLEX, 20 MM PHOSPHATE REMARK 210 BUFFER, 56 MM NACL, PH 6.8-7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : MORASS 2.5 REMARK 210 METHOD USED : MATRIX RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : SUBMITTED THE AVERAGE STRUCTURE REMARK 210 OF THE 10 STRUCTURES DETERMINED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES. 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 OP2 DA A 6 HO3 BAP A 25 1.44 REMARK 500 HO5' DT B 13 OP2 DG B 14 1.46 REMARK 500 OP2 DA A 6 HO2 BAP A 25 1.60 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 DA A 6 C5' DA A 6 C4' 0.047 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 DT A 1 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 DT A 1 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES REMARK 500 DA A 2 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA A 2 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG A 3 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES REMARK 500 DC A 5 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 9 N1 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA A 12 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA A 12 N1 - C6 - N6 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DT B 13 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 15 O4' - C4' - C3' ANGL. DEV. = 6.1 DEGREES REMARK 500 DC B 16 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 19 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 DT B 19 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 21 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DC B 22 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 23 O4' - C4' - C3' ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 24 N1 - C6 - N6 ANGL. DEV. = -4.3 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 5 0.12 SIDE CHAIN REMARK 500 DA A 6 0.08 SIDE CHAIN REMARK 500 DA A 7 0.12 SIDE CHAIN REMARK 500 DG A 9 0.08 SIDE CHAIN REMARK 500 DC A 11 0.08 SIDE CHAIN REMARK 500 DG B 14 0.07 SIDE CHAIN REMARK 500 DT B 19 0.16 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 BAP A 25 DBREF 1FYY A 1 12 PDB 1FYY 1FYY 1 12 DBREF 1FYY B 13 24 PDB 1FYY 1FYY 13 24 SEQRES 1 A 12 DT DA DG DT DC DA DA DG DG DG DC DA SEQRES 1 B 12 DT DG DC DC DC DT DT DG DA DC DT DA HET BAP A 25 38 HETNAM BAP 1,2,3-TRIHYDROXY-1,2,3,4-TETRAHYDROBENZO[A]PYRENE FORMUL 3 BAP C20 H16 O3 LINK N6 DA A 7 C4' BAP A 25 1555 1555 1.49 SITE 1 AC1 5 DC A 5 DA A 6 DA A 7 DT B 18 SITE 2 AC1 5 DT 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 - 23 202 Bytes