Header list of 1gip.pdb file
Complete list - 23 20 Bytes
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
MODEL 1
Complete list - 23 20 Bytes