10 20 30 40 50 60 70 80 2HSL - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 22-JUL-06 2HSL
TITLE NMR STRUCTURE OF 13MER DUPLEX DNA CONTAINING AN ABASIC SITE, TITLE 2 AVERAGED STRUCTURE (ALPHA ANOMER)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*CP*AP*AP*AP*GP*(D1P)P*AP*CP*CP*GP*GP*G)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*CP*CP*GP*GP*TP*AP*CP*TP*TP*TP*GP*G)-3'; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS ABASIC SITE, DNA LESION, BASE EXCISION REPAIR, APE1
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR J.CHEN,F.Y.DUPRADEAU,D.A.CASE,C.J.TURNER,J.STUBBE
REVDAT 2 24-FEB-09 2HSL 1 VERSN REVDAT 1 29-MAY-07 2HSL 0
JRNL AUTH J.CHEN,F.Y.DUPRADEAU,D.A.CASE,C.J.TURNER,J.STUBBE JRNL TITL NUCLEAR MAGNETIC RESONANCE STRUCTURAL STUDIES AND JRNL TITL 2 MOLECULAR MODELING OF DUPLEX DNA CONTAINING NORMAL JRNL TITL 3 AND 4'-OXIDIZED ABASIC SITES. JRNL REF BIOCHEMISTRY V. 46 3096 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17323932 JRNL DOI 10.1021/BI6024269
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0 REMARK 3 AUTHORS : CASE, ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 482 NOE- REMARK 3 DERIVED DISTANCE CONSTRAINTS, 57 DIHEDRAL ANGLE RESTRAINTS,8 REMARK 3 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
REMARK 4 REMARK 4 2HSL COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB038711.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 277 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 10 MM SODIUM PHOSPHATE; 10 MM REMARK 210 SODIUM PHOSPHATE REMARK 210 PRESSURE : 1ATM; 1ATM REMARK 210 SAMPLE CONTENTS : 2.7 MM IN 10 MM SODIUM REMARK 210 PHOSPHATE, 0.2 MM EDTA, D2O; REMARK 210 2.7 MM IN 10 MM SODIUM REMARK 210 PHOSPHATE, 0.2 MM EDTA, 90% REMARK 210 H2O/10% D2O(V/V) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, E-COSY, H REMARK 210 -P-SELECTIVE HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ, 591 MHZ REMARK 210 SPECTROMETER MODEL : CUSTOM-BUILT REMARK 210 SPECTROMETER MANUFACTURER : CUSTOM-BUILT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 2000, MARDIGRAS REMARK 210 METHOD USED : SIMULATED ANNEALING MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL 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 AND HP-HSQC 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 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. = 3.3 DEGREES REMARK 500 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 2 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA A 3 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA A 3 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 3 N1 - C6 - N6 ANGL. DEV. = -4.5 DEGREES REMARK 500 DA A 4 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA A 4 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 4 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DA A 5 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA A 5 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA A 5 N1 - C6 - N6 ANGL. DEV. = -4.7 DEGREES REMARK 500 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA A 8 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DA A 8 N1 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 DC A 9 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 DC A 10 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 14 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC B 14 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 15 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DC B 16 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 16 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA B 20 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 20 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 DA B 20 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA B 20 N1 - C6 - N6 ANGL. DEV. = -5.9 DEGREES REMARK 500 DC B 21 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 23 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 DT B 24 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 DG B 25 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 26 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 D1P IS AN ALPHA ANOMER. THEREFORE, C1' CENTER HAS CORRECT REMARK 600 CHIRALITY AT D1P.
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HSK RELATED DB: PDB REMARK 900 RELATED ID: 2HOU RELATED DB: PDB REMARK 900 RELATED ID: 2HPX RELATED DB: PDB REMARK 900 RELATED ID: 2HSR RELATED DB: PDB REMARK 900 RELATED ID: 2HSS RELATED DB: PDB
DBREF 2HSL A 1 13 PDB 2HSL 2HSL 1 13 DBREF 2HSL B 14 26 PDB 2HSL 2HSL 14 26
SEQRES 1 A 13 DC DC DA DA DA DG ORP DA DC DC DG DG DG SEQRES 1 B 13 DC DC DC DG DG DT DA DC DT DT DT DG DG
HET ORP A 7 20
HETNAM ORP 2-DEOXY-5-PHOSPHONO-RIBOSE
FORMUL 1 ORP C5 H11 O7 P
LINK O3' DG A 6 P ORP A 7 1555 1555 1.60 LINK O3 ORP A 7 P DA A 8 1555 1555 1.60
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