10 20 30 40 50 60 70 80 1KXS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 01-FEB-02 1KXS
TITLE NMR STUDY OF B-DNA CONTAINING A MODIFIED BASE PAIR: THE 2'- TITLE 2 DEOXYADENOSINE 3-(2-HYDROXYETHYL-2'-DEOXYURIDINE)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*AP*GP*TP*CP*(HEU) COMPND 3 P*AP*AP*AP*AP*CP*G)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*GP*TP*TP*TP*TP*AP*GP*AP*CP*TP*TP*GP*C)- COMPND 8 3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES
KEYWDS MODIFIED BASE, MUTAGENESIS, DEOXYRIBONUCLEIC ACID, DNA
EXPDTA SOLUTION NMR
NUMMDL 2
AUTHOR Y.BOULARD,G.V.FAZAKERLEY,L.C.SOWERS
REVDAT 3 24-FEB-09 1KXS 1 VERSN REVDAT 2 13-MAR-02 1KXS 1 JRNL REVDAT 1 06-MAR-02 1KXS 0
JRNL AUTH Y.BOULARD,G.V.FAZAKERLEY,L.C.SOWERS JRNL TITL THE SOLUTION STRUCTURE OF AN OLIGONUCLEOTIDE JRNL TITL 2 DUPLEX CONTAINING A JRNL TITL 3 2'-DEOXYADENOSINE-3-(2-HYDROXYETHYL)- JRNL TITL 4 2'-DEOXYURIDINE BASE PAIR DETERMINED BY NMR AND JRNL TITL 5 MOLECULAR DYNAMICS STUDIES. JRNL REF NUCLEIC ACIDS RES. V. 30 1371 2002 JRNL REFN ISSN 0305-1048 JRNL PMID 11884635 JRNL DOI 10.1093/NAR/30.6.1371
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, MORCAD AND OCL, MOLMOL 2.6 REMARK 3 AUTHORS : KOLLMAN (AMBER), LEBRET (MORCAD AND OCL), REMARK 3 KORADI (MOLMOL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1KXS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-02. REMARK 100 THE RCSB ID CODE IS RCSB015447.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : 10 MM PHOSPHATE BUFFER, 5 REMARK 210 NACL, 0.2 MM EDTA REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM DNA, 10 MM PHOSPHATE REMARK 210 BUFFER, 50 MM NACL, 0.5 MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, TOCSY, REMARK 210 HSQC 1H-31P REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.5 REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNA REMARK 210 SIMULATIONS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 256 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : FIT WITH NMR CONSTRAINTS AND REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURES WERE DETERMINED USING PROTON NMR REMARK 210 FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS REMARK 210 SIMULATIONS. THE BEST REPRESENTATIVE STRUCTURES ARE PRESENTED, REMARK 210 MODELS 1 AND 2.
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 1 DC B 15 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DT B 20 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DA B 21 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 25 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 26 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 20 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT B 25 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 26 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DC B 28 O4' - C1' - N1 ANGL. DEV. = 1.8 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 1 DA B 21 0.06 SIDE_CHAIN REMARK 500 1 DG B 27 0.07 SIDE_CHAIN REMARK 500 2 DT A 6 0.06 SIDE_CHAIN REMARK 500 2 DA B 23 0.05 SIDE_CHAIN REMARK 500 2 DG B 27 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
DBREF 1KXS A 1 14 PDB 1KXS 1KXS 1 14 DBREF 1KXS B 15 28 PDB 1KXS 1KXS 15 28
SEQRES 1 A 14 DG DC DA DA DG DT DC HEU DA DA DA DA DC SEQRES 2 A 14 DG SEQRES 1 B 14 DC DG DT DT DT DT DA DG DA DC DT DT DG SEQRES 2 B 14 DC
MODRES 1KXS HEU A 8 DU
HET HEU A 8 36
HETNAM HEU 3-(2-HYDROXYETHYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
FORMUL 1 HEU C11 H17 N2 O9 P
LINK O3' DC A 7 P HEU A 8 1555 1555 1.62 LINK O3' HEU A 8 P DA A 9 1555 1555 1.62
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