Header list of 1s9n.pdb file
Complete list - r 2 2 Bytes
HEADER DNA 05-FEB-04 1S9N TITLE SOLUTION STRUCTURE OF THE NITROUS ACID (G)-(G) CROSS-LINKED DNA TITLE 2 DODECAMER DUPLEX GCATCC(G)GATGC COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*CP*CP*GP*GP*AP*TP*GP*C)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED ACCORDING TO HARWOOD ET SOURCE 4 AL.(1999) J. AM. CHEM. SOC. 121, 5081-5082 KEYWDS DNA, CROSS-LINK, NITROUS ACID, EXTRAHELICAL CYTOSINES, MINOR GROOVE EXPDTA SOLUTION NMR NUMMDL 26 AUTHOR N.B.F.EDFELDT,E.A.HARWOOD,S.T.SIGURDSSON,P.B.HOPKINS,B.R.REID REVDAT 3 02-MAR-22 1S9N 1 REMARK LINK REVDAT 2 24-FEB-09 1S9N 1 VERSN REVDAT 1 21-JUN-05 1S9N 0 JRNL AUTH N.B.F.EDFELDT,E.A.HARWOOD,S.T.SIGURDSSON,P.B.HOPKINS, JRNL AUTH 2 B.R.REID JRNL TITL SOLUTION STRUCTURE OF A NITROUS ACID INDUCED DNA INTERSTRAND JRNL TITL 2 CROSS-LINK JRNL REF NUCLEIC ACIDS RES. V. 32 2785 2004 JRNL REFN ISSN 0305-1048 JRNL PMID 15155847 JRNL DOI 10.1093/NAR/GKH606 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER 1 REMARK 3 AUTHORS : BRUKER (XWINNMR), BIOSYM (DISCOVER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 715 DISTANCE RESTRAINTS (560 ARE NOE-DERIVED, 52 BASED ON REMARK 3 HYDROGEN BONDING, 103 REPULSIVE) AND 178 DIHEDRAL ANGLE REMARK 3 RESTRAINTS (106 BACKBONE AND 72 CHIRAL). REMARK 4 REMARK 4 1S9N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021540. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 200MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM DNA, 10MM PHOSPHATE PH 7.0, REMARK 210 200MM NACL, 1MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; H-P HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 1, DGII 1, DISCOVER 1, REMARK 210 BIRDER 1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 RELAXATION MATRIX REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 26 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-26 REMARK 470 RES CSSEQI ATOMS REMARK 470 DG B 7 N2 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 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 1 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 2 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 3 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 4 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 5 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 6 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 7 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 8 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 9 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 10 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 11 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 12 DG B 7 C6 DG B 7 O6 0.126 REMARK 500 13 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 14 DG B 7 C6 DG B 7 O6 0.125 REMARK 500 15 DG A 7 C6 DG A 7 O6 0.125 REMARK 500 16 DG A 7 C6 DG A 7 O6 0.125 REMARK 500 17 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 18 DG A 7 C6 DG A 7 O6 0.125 REMARK 500 19 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 20 DG A 7 C6 DG A 7 O6 0.125 REMARK 500 21 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 22 DG A 7 C6 DG A 7 O6 0.125 REMARK 500 23 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 24 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 25 DG A 7 C6 DG A 7 O6 0.126 REMARK 500 26 DG A 7 C6 DG A 7 O6 0.125 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 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DG B 7 N1 - C2 - N2 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG B 7 C5 - C6 - O6 ANGL. DEV. = -6.0 DEGREES REMARK 500 1 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DT B 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DG B 7 N1 - C2 - N2 ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DG B 7 C5 - C6 - O6 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT B 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DC A 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG A 11 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 3 DG B 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DT B 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DT B 4 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 3 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG B 7 N1 - C2 - N2 ANGL. DEV. = 5.6 DEGREES REMARK 500 3 DG B 7 C5 - C6 - O6 ANGL. DEV. = -6.0 DEGREES REMARK 500 3 DG B 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DT B 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 3 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 4 DG A 1 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DT A 4 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 413 ANGLE DEVIATIONS. 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 1 DA A 3 0.09 SIDE CHAIN REMARK 500 1 DT A 4 0.07 SIDE CHAIN REMARK 500 1 DC A 6 0.08 SIDE CHAIN REMARK 500 1 DG A 11 0.07 SIDE CHAIN REMARK 500 1 DA B 3 0.09 SIDE CHAIN REMARK 500 1 DT B 4 0.07 SIDE CHAIN REMARK 500 1 DC B 6 0.08 SIDE CHAIN REMARK 500 1 DG B 7 0.10 SIDE CHAIN REMARK 500 1 DG B 11 0.07 SIDE CHAIN REMARK 500 2 DA A 3 0.09 SIDE CHAIN REMARK 500 2 DT A 4 0.07 SIDE CHAIN REMARK 500 2 DC A 6 0.08 SIDE CHAIN REMARK 500 2 DG A 11 0.07 SIDE CHAIN REMARK 500 2 DA B 3 0.09 SIDE CHAIN REMARK 500 2 DT B 4 0.07 SIDE CHAIN REMARK 500 2 DC B 6 0.08 SIDE CHAIN REMARK 500 2 DG B 7 0.10 SIDE CHAIN REMARK 500 2 DG B 11 0.07 SIDE CHAIN REMARK 500 3 DA A 3 0.09 SIDE CHAIN REMARK 500 3 DT A 4 0.07 SIDE CHAIN REMARK 500 3 DC A 6 0.08 SIDE CHAIN REMARK 500 3 DG A 11 0.07 SIDE CHAIN REMARK 500 3 DA B 3 0.09 SIDE CHAIN REMARK 500 3 DT B 4 0.07 SIDE CHAIN REMARK 500 3 DC B 6 0.08 SIDE CHAIN REMARK 500 3 DG B 7 0.11 SIDE CHAIN REMARK 500 3 DG B 11 0.07 SIDE CHAIN REMARK 500 4 DA A 3 0.09 SIDE CHAIN REMARK 500 4 DT A 4 0.07 SIDE CHAIN REMARK 500 4 DC A 6 0.08 SIDE CHAIN REMARK 500 4 DG A 11 0.07 SIDE CHAIN REMARK 500 4 DA B 3 0.09 SIDE CHAIN REMARK 500 4 DT B 4 0.06 SIDE CHAIN REMARK 500 4 DC B 6 0.08 SIDE CHAIN REMARK 500 4 DG B 7 0.10 SIDE CHAIN REMARK 500 4 DG B 11 0.07 SIDE CHAIN REMARK 500 5 DA A 3 0.09 SIDE CHAIN REMARK 500 5 DT A 4 0.07 SIDE CHAIN REMARK 500 5 DC A 6 0.08 SIDE CHAIN REMARK 500 5 DG A 11 0.07 SIDE CHAIN REMARK 500 5 DA B 3 0.09 SIDE CHAIN REMARK 500 5 DT B 4 0.07 SIDE CHAIN REMARK 500 5 DC B 6 0.08 SIDE CHAIN REMARK 500 5 DG B 7 0.10 SIDE CHAIN REMARK 500 5 DG B 11 0.07 SIDE CHAIN REMARK 500 6 DA A 3 0.09 SIDE CHAIN REMARK 500 6 DT A 4 0.07 SIDE CHAIN REMARK 500 6 DC A 6 0.08 SIDE CHAIN REMARK 500 6 DG A 11 0.07 SIDE CHAIN REMARK 500 6 DA B 3 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 231 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1S9N A 1 12 PDB 1S9N 1S9N 1 12 DBREF 1S9N B 1 12 PDB 1S9N 1S9N 1 12 SEQRES 1 A 12 DG DC DA DT DC DC DG DG DA DT DG DC SEQRES 1 B 12 DG DC DA DT DC DC DG DG DA DT DG DC LINK C2 DG A 7 N2 DG B 7 1555 1555 1.35 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 MODEL 1
Complete list - r 2 2 Bytes