PDB Short entry for 1GIP HEADER DNA 20-FEB-01 1GIP TITLE THE NMR STRUCTURE OF DNA DODECAMER DETERMINED IN AQUEOUS DILUTE LIQUID TITLE 2 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 B-DNA, DIPOLAR COUPLING, NOE, BASE-BASE ORIENTATIONAL POTENTIAL OF KEYWDS 2 MEAN FORCE, DATABASE TORSION ANGLE POTENTIAL OF MEAN FORCE, DNA EXPDTA SOLUTION NMR NUMMDL 2 AUTHOR G.M.CLORE,J.KUSZEWSKI REVDAT 3 23-FEB-22 1GIP 1 REMARK REVDAT 2 24-FEB-09 1GIP 1 VERSN REVDAT 1 01-AUG-01 1GIP 0 JRNL AUTH J.KUSZEWSKI,C.SCHWIETERS,G.M.CLORE JRNL TITL IMPROVING THE ACCURACY OF NMR STRUCTURES OF DNA BY MEANS OF JRNL TITL 2 A DATABASE POTENTIAL OF MEAN FORCE DESCRIBING BASE-BASE JRNL TITL 3 POSITIONAL INTERACTIONS. JRNL REF J.AM.CHEM.SOC. V. 123 3903 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11457140 JRNL DOI 10.1021/JA010033U REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.TJANDRA,S.TATE,A.ONO,M.KAINOSHO,A.BAX REMARK 1 TITL THE NMR STRUCTURE OF A DNA DODECAMER IN AN AQUEOUS DILUTE REMARK 1 TITL 2 LIQUID CRYSTALLINE PHASE REMARK 1 REF J.AM.CHEM.SOC. V. 122 6190 2000 REMARK 1 REFN ISSN 0002-7863 REMARK 1 DOI 10.1021/JA000324N REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NIH VERSION OF XPLOR (AVAILABLE TO ACADEMIC USERS REMARK 3 BY ANONYMOUS FTP AT PORTAL.NIDDK.NIH.GOV IN PUB/ REMARK 3 CLORE/XPLOR_NIH) REMARK 3 AUTHORS : CLORE, SCHWIETERS AND KUSZEWSKI. ADAPTED FROM REMARK 3 XPLOR 3.841 BY BRUNGER ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE IS BASED ON A REMARK 3 TOTAL OF 162 NOE, 48 DISTANCES FOR WATSON-CRICK HYDROGEN BONDS, REMARK 3 AND 137 DIHEDRAL REMARK 3 137 TORSION ANGLE RESTRAINTS, 198 CH AND 10 NH ONE-BOND DIPOLAR REMARK 3 COUPLING RESTRAINTS, AND 200 APPROXIMATE PROTON-PROTON REMARK 3 DIPOLAR COUPLINGS. THE EXPERIMENTAL RESTRAINTS ARE THE SAME AS REMARK 3 THOSE REMARK 3 LISTED IN 1DUF. THE NON-BONDED CONTACTS ARE REPRESENTED REMARK 3 BY A QUARTIC VAN DER WAALS REPULSION TERM AND A BASE-BASE REMARK 3 POSITIONING REMARK 3 DATABASE POTENTIAL OF MEAN FORCE. ALSO INCLUDED IS A TORSION ANGLE REMARK 3 DATABASE POTENTIAL OF MEAN FORCE. REMARK 3 REMARK 3 IN THIS ENTRY THE SECOND TO LAST COLUMN REPRESENTS THE REMARK 3 AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED REMARK 3 ANNEALING STRUCTURES AND THE MEAN COORDINATE POSITIONS. REMARK 3 REMARK 3 MODEL 1 IS CALCULATED WITH NOE-DERIVED INTERPROTON REMARK 3 DISTANCE RESTRAINTS, DIPOLAR COUPLING REMARK 3 RESTRAINTS AND TORSION ANGLE RESTRAINTS. REMARK 3 MODEL 2 IS CALCULATED WITH DIPOLAR COUPLING AND TORSION REMARK 3 ANGLE RESTRAINTS. NO NOE-DERIVED INTERPROTON REMARK 3 DISTANCE RESTRAINTS WERE EMPLOYED. REMARK 3 REMARK 3 STRUCTURAL STATISTICS: REMARK 3 ---------------------------------------------------------- REMARK 3 RESTRAINTS MODEL 1 MODEL 2 REMARK 3 (# MODEL 1/# MODEL 2) (NOE + DIPOLARS) (DIPOLARS ONLY) REMARK 3 ---------------------------------------------------------- REMARK 3 RMS DEVIATIONS FROM EXPERIMENTAL RESTRAINTS REMARK 3 INTERPROTON DISTANCES (A) 0.065 0.114 REMARK 3 (162/0) REMARK 3 TORSION ANGLES (DEG) 0 0 REMARK 3 (137/137) REMARK 3 ALL DIPOLAR COUPLINGS (HZ) 2.8 2.6 REMARK 3 (408/408) REMARK 3 RMS DEVIATIONS AND DIPOLAR COUPLING R-FACTORS REMARK 3 FOR DIFFERENT CLASSES OF DIPOLAR COUPLINGS REMARK 3 C-H RIBOSE (HZ/%) (94/94)* 2.27 (11.4%) 2.27 (11.4%) REMARK 3 C-H RIBOSE (HZ/%) (64/64)** 5.62 (28.1%) 5.24 (26.2%) REMARK 3 C-H BASE (HZ/%) (24/24)* 2.78 (13.9%) 2.81 (14.1%) REMARK 3 C-H BASE (HZ/%) (12/12)** 1.89 (9.26%) 2.01 (10.0%) REMARK 3 C-H METHYL (HZ/%) (4/4)* 0.98 (4.9%) 0.79 (4.0%) REMARK 3 N-H IMINO (HZ/%) (10/10)* 1.56 (15.9%) 1.50 (15.2%) REMARK 3 H-H ABSOLUTE VALUE (HZ) REMARK 3 (126/126) 1.26 1.25 REMARK 3 H-H SIGN KNOWN (HZ) (74/74) 0.93 0.88 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEALIZED COVALENT GEOMETRY REMARK 3 BONDS (A) 0.003 0.003 REMARK 3 ANGLES (DEG) 0.897 0.925 REMARK 3 IMPROPER TORSIONS (DEG) 0.296 0.106 REMARK 3 ---------------------------------------------------------- REMARK 3 * MEASURED WITH AN ACCURACY OF +/- 2 HZ REMARK 3 ** MEASURED WITH AN ACCURACY OF +/- 4 HZ REMARK 3 DIPOLAR COUPLING R-FACTOR = RATIO RMS DEVIATION BETWEEN REMARK 3 OBSERVED AND CALCULATED VALUES AND EXPECTED RMS DEVIATION REMARK 3 IF VECTORS ARE RANDOMLY DISTRIBUTED. THE LATTER IS GIVEN REMARK 3 BY {2DA**2[4 + 3H**2]/5}1/2 WHERE DA IS THE MAGNITUDE OF REMARK 3 THE AXIAL COMPONENT OF THE ALIGNMENT TENSOR AND H IS THE REMARK 3 RHOMBICITY. (ONLY APPLIES TO FIXED LENGTH VECTORS). THE REMARK 3 VALUES OF DA(CH), DA(NH) AND H ARE -16 HZ, -7.7 HZ AND REMARK 3 0.26, RESPECTIVELY. REMARK 4 REMARK 4 1GIP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000001558. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308.00 REMARK 210 PH : 7.00 REMARK 210 IONIC STRENGTH : 40 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM DUPLEX DNA, 40MM SODIUM REMARK 210 PHOSPHATE, PH 7.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 13C-HSQC-J-MODULATED; COSY; 13C REMARK 210 -HSQC-F1- COUPLED; 15N-HSQC-F1- REMARK 210 COUPLED; 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7 1999.039.11.31, REMARK 210 XWINNMR 2.4, PIPP/CAPP 4.2.8 REMARK 210 METHOD USED : SIMULATED ANNEALING IN TORSION REMARK 210 ANGLE SPACE USING A SIXTH ORDER REMARK 210 PREDICTOR-CORRECTOR METHOD WITH REMARK 210 AUTOMATIC TIME STEP SELECTION REMARK 210 (C. SCHWIETERS AND G.M. CLORE) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 2 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE RESTRAINED REGULARIZED MEAN REMARK 210 STRUCTURES REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: REMARK 210 THE NUMBER OF CALCULATED CONFORMERS IS 20 WITH NOES AND DIPOLAR REMARK 210 COUPLINGS REMARK 210 AND 20 WITH DIPOLAR COUPLINGS ONLY 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 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BNA RELATED DB: PDB REMARK 900 DREW AND DICKERSON DODECAMER REMARK 900 RELATED ID: 355D RELATED DB: PDB REMARK 900 HIGH RESOLUTION DREW AND DICKERSON DODECAMER REMARK 900 RELATED ID: 1DUF RELATED DB: PDB REMARK 900 DODECAMER DETERMINED FROM DIPOLAR COUPLINGS DBREF 1GIP A 1 12 PDB 1GIP 1GIP 1 12 DBREF 1GIP B 13 24 PDB 1GIP 1GIP 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