HEADER DNA 27-NOV-02 1NAJ TITLE HIGH RESOLUTION NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS TITLE 2 DILUTE LIQUID CRYSTALLINE PHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DICKERSON DODECAMER, DNA EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR Z.WU,F.DELAGLIO,N.TJANDRA,V.ZHURKIN,A.BAX REVDAT 4 22-MAY-24 1NAJ 1 REMARK REVDAT 3 23-FEB-22 1NAJ 1 REMARK REVDAT 2 24-FEB-09 1NAJ 1 VERSN REVDAT 1 08-JUL-03 1NAJ 0 JRNL AUTH Z.WU,F.DELAGLIO,N.TJANDRA,V.B.ZHURKIN,A.BAX JRNL TITL OVERALL STRUCTURE AND SUGAR DYNAMICS OF A DNA DODECAMER FROM JRNL TITL 2 HOMO- AND HETERONUCLEAR DIPOLAR COUPLINGS AND (31)P CHEMICAL JRNL TITL 3 SHIFT ANISOTROPY. JRNL REF J.BIOMOL.NMR V. 26 297 2003 JRNL REFN ISSN 0925-2738 JRNL PMID 12815257 JRNL DOI 10.1023/A:1024047103398 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 1.7 REV 1999.039.11.31, X-PLOR 3.841 REMARK 3 AUTHORS : DELAGLIO, FRANK (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 162 NOE, 32 HYDROGEN BOND, REMARK 3 AND 24 DIHEDRAL RESTRAINTS; AS WELL AS 262 CH AND 16 NH ONE-BOND REMARK 3 DIPOLAR COUPLING RESTRAINTS, 200 APPROXIMATE PROTON-PROTON DIPOLAR REMARK 3 COUPLINGS, 300 QUANTITATIVE PROTON-PROTON DIPOLAR RESTRAINTS, 22 REMARK 3 31P-1H REMARK 3 DIPOLAR COUPLINGS, AND 22 31P CHEMICAL SHIFT ANISOTROPY RESTRAINTS. REMARK 3 REMARK 3 THE COORDINATE OF THE ALIGNMENT TENSOR IS DEFINED BY MOLECULE 500 REMARK 3 AND 501. REMARK 4 REMARK 4 1NAJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-DEC-02. REMARK 100 THE DEPOSITION ID IS D_1000017718. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 40MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM UNLABELED DUPLEX DNA, REMARK 210 40MM SODIUM PHOSPHATE, PH 7.0; REMARK 210 0.5 MM U-13C/15N DUPLEX DNA, REMARK 210 40MM SODIUM PHOSPHATE, PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : H-31P-HSQC, HP-CTNOESY-DIF, REMARK 210 COSY; COSY,2D NOESY,13C-HSQC-J-MODULATED,13C-HSQC-F1-COUPLED, REMARK 210 15N-HSQC-F1-COUPLED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR VERSION 2.4 AND 2.6, REMARK 210 COSYVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3 REMARK 210 REMARK 210 REMARK: NULL 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 H21 DG A 2 O2 DC B 23 1.56 REMARK 500 O2 DC A 11 H21 DG B 14 1.57 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 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 1 DG A 2 C4' - C3' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DC A 3 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DA A 6 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DT A 7 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DT A 8 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DC A 9 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DC A 11 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 1 DG A 12 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DC B 13 C4' - C3' - C2' ANGL. DEV. = 7.2 DEGREES REMARK 500 1 DG B 14 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DC B 15 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG B 16 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DA B 18 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 1 DT B 19 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT B 20 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 DC B 21 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DC B 23 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 1 DG B 24 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 2 DC A 1 C4' - C3' - C2' ANGL. DEV. = 7.1 DEGREES REMARK 500 2 DG A 2 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DC A 3 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DG A 4 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DA A 6 C4' - C3' - C2' ANGL. DEV. = 6.1 DEGREES REMARK 500 2 DT A 7 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 8 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DC A 9 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DG A 10 C4' - C3' - C2' ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DC A 11 C4' - C3' - C2' ANGL. DEV. = 6.8 DEGREES REMARK 500 2 DG A 12 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DC B 13 C4' - C3' - C2' ANGL. DEV. = 7.1 DEGREES REMARK 500 2 DG B 14 C4' - C3' - C2' ANGL. DEV. = 5.6 DEGREES REMARK 500 2 DC B 15 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 2 DG B 16 C4' - C3' - C2' ANGL. DEV. = 5.5 DEGREES REMARK 500 2 DA B 18 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DT B 19 C4' - C3' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 2 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT B 20 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 2 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 DC B 21 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 2 DG B 22 C4' - C3' - C2' ANGL. DEV. = 5.4 DEGREES REMARK 500 2 DC B 23 C4' - C3' - C2' ANGL. DEV. = 6.9 DEGREES REMARK 500 2 DG B 24 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 3 DC A 1 C4' - C3' - C2' ANGL. DEV. = 6.9 DEGREES REMARK 500 3 DG A 2 C4' - C3' - C2' ANGL. DEV. = 5.4 DEGREES REMARK 500 3 DC A 3 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 108 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BNA RELATED DB: PDB REMARK 900 RELATED ID: 355D RELATED DB: PDB REMARK 900 RELATED ID: 1DUF RELATED DB: PDB DBREF 1NAJ A 1 12 PDB 1NAJ 1NAJ 1 12 DBREF 1NAJ B 13 24 PDB 1NAJ 1NAJ 13 24 SEQRES 1 A 12 DC DG DC DG DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC DG DA DA DT DT DC DG DC DG 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