Header list of 1n1n.pdb file
Complete list - 23 202 Bytes
HEADER DNA 18-OCT-02 1N1N TITLE STRUCTURE OF MISPAIRING OF THE DEOXYCYTOSINE WITH DEOXYADENOSINE 5' TO TITLE 2 THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*AP*TP*CP*GP*AP*TP*CP*T)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*AP*GP*AP*TP*CP*AP*AP*TP*GP*T)-3'; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: ENGINEERED SYNTHETIC OLIGO NULCEOTIDE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: SYNTHETIC OLIGO NULCEOTIDE KEYWDS AFLATOXIN B1 ADDUCT 5' TO AC MISMATCH, MAJOR CONFORMATION, DNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR M.P.STONE,I.GIRI REVDAT 3 23-FEB-22 1N1N 1 REMARK LINK REVDAT 2 24-FEB-09 1N1N 1 VERSN REVDAT 1 28-OCT-03 1N1N 0 JRNL AUTH I.GIRI,M.P.STONE JRNL TITL WOBBLE DC.DA PAIRING 5' TO THE CATIONIC GUANINE N7 JRNL TITL 2 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 ADDUCT: JRNL TITL 3 IMPLICATIONS FOR NONTARGETED AFB1 MUTAGENESIS. JRNL REF BIOCHEMISTRY V. 42 7023 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12795597 JRNL DOI 10.1021/BI020688N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 6.5, AMBER 6.0 REMARK 3 AUTHORS : BRUNGER (X-PLOR), CASE (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE WAS CALCULATED USING RANDMARDI REMARK 3 PROTOCOL FROM MARDIGRAS. THE 20 STRUCTURES OBTAINED FROM REMARK 3 MOLECULAR DYNAMICS SIMULATION USING X-PLOR STARTING FROM RANDOM, REMARK 3 AND B-STARTING STRUCTURES. THE FINAL STRUCTURE EMERGED FROM REMARK 3 AVERAGE OF 20 SIMULATED ANNEALING STRUCTURE FROM B-FORM STARTING REMARK 3 STRUCTURE. THE AVERAGE STRUCTURE WAS SOLVATED USING X-LEAP REMARK 3 PROTOCOL IN AMBER 6.0, AND SUBJECTED TO 1.4 NS MD SIMULATION REMARK 3 USING AMBER 6.0 SANDER MODULE, IN PRESENCE OF COUNTER IONS. THE REMARK 3 FINAL STRUCTURE WAS OBTAINED BY ENERGY MINIMIZATION OF SIMULATED REMARK 3 STRUCTURE. SOLVENT, AND COUNTER IONS WERE OMITTED. BACK REMARK 3 CALCULATIONS WERE PERFORMED USING CORMA. REMARK 4 REMARK 4 1N1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-02. REMARK 100 THE DEPOSITION ID IS D_1000017406. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 278; 278 REMARK 210 PH : 7.2; 6.7; 7.2 REMARK 210 IONIC STRENGTH : 0.01 M SODIUM PHOSPHATE BUFFER REMARK 210 CONTAINING 0.1 M NACL AND 0.05 REMARK 210 MM NA2EDTA; 0.01 M SODIUM REMARK 210 PHOSPHATE BUFFER CONTAINING 0.1 REMARK 210 M NACL AND 0.05 MM NA2EDTA; 0.01 REMARK 210 M SODIUM PHOSPHATE BUFFER REMARK 210 CONTAINING 0.1 M NACL AND 0.05 REMARK 210 MM NA2EDTA REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : THE SAMPLE WAS DISSOLVED IN 0.5 REMARK 210 ML OF 0.01 M SODIUM PHOSPHATE REMARK 210 BUFFER FOR NMR CONTAINING 0.1 M REMARK 210 NACL AND 0.05 MM NA2EDTA AT PH REMARK 210 7.2; THE SAMPLE WAS DISSOLVED IN REMARK 210 0.5 ML OF 0.01 M SODIUM REMARK 210 PHOSPHATE BUFFER CONTAINING 0.1 REMARK 210 M NACL AND 0.05 MM NA2EDTA AT PH REMARK 210 6.7 FOR NMR STUDIES; THE AMPLE REMARK 210 WAS DISSOLVED IN 0.5 ML OF 0.01 REMARK 210 M SODIUM PHOSPHATE BUFFER REMARK 210 CONTAINING 0.1 M NACL AND 0.05 REMARK 210 MM NA2EDTA AT PH 7.2 FOR NMR REMARK 210 STUDIES REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; P-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : INSIGHT II 2000, FELIX 97, 2000, REMARK 210 MARDIGRAS 5.2, 6.2, XWINNMR 3 REMARK 210 METHOD USED : DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING NMR DATA : FELIX 97, REMARK 210 2000 MOLECULAR DYNAMICS : XPLOR, REMARK 210 AMBER MATRIX RELAXATION CORMA REMARK 210 TORSION ANGLE DYNAMICS GAUSSIAN REMARK 210 98, INSIGHTII (2000) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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: 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 DA A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 1 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 DT A 4 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DT A 4 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DC A 5 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 7 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DT A 8 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DA B 11 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 11 N1 - C6 - N6 ANGL. DEV. = -5.0 DEGREES REMARK 500 DA B 13 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DC B 15 N1 - C2 - O2 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 16 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DA B 16 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA B 16 N1 - C6 - N6 ANGL. DEV. = -9.8 DEGREES REMARK 500 DA B 16 C5 - C6 - N6 ANGL. DEV. = 6.3 DEGREES REMARK 500 DA B 17 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA B 17 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA B 17 N1 - C6 - N6 ANGL. DEV. = -4.1 DEGREES REMARK 500 DT B 18 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT B 18 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 19 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG B 19 N1 - C6 - O6 ANGL. DEV. = -3.8 DEGREES REMARK 500 DT B 20 C6 - C5 - C7 ANGL. DEV. = -4.1 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 0.06 SIDE CHAIN REMARK 500 DG A 6 0.14 SIDE CHAIN REMARK 500 DA A 7 0.06 SIDE CHAIN REMARK 500 DC A 9 0.07 SIDE CHAIN REMARK 500 DC B 15 0.13 SIDE CHAIN REMARK 500 DT B 18 0.10 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 AFN A 26 DBREF 1N1N A 1 10 PDB 1N1N 1N1N 1 10 DBREF 1N1N B 11 20 PDB 1N1N 1N1N 11 20 SEQRES 1 A 10 DA DC DA DT DC DG DA DT DC DT SEQRES 1 B 10 DA DG DA DT DC DA DA DT DG DT HET AFN A 26 37 HETNAM AFN 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 FORMUL 3 AFN C17 H14 O7 LINK N7 DG A 6 C8A AFN A 26 1555 1555 1.51 SITE 1 AC1 4 DC A 5 DG A 6 DC B 15 DA B 16 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