Header list of 1d19.pdb file
Complete list - 16 202 Bytes
HEADER DNA 01-AUG-90 1D19
TITLE SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS USING NUCLEAR
TITLE 2 MAGNETIC RESONANCE, RESTRAINED MOLECULAR DYNAMICS AND NOE-BASED
TITLE 3 REFINEMENT
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(*GP*TP*AP*CP*GP*TP*AP*C)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DNA, DOUBLE HELIX
EXPDTA SOLUTION NMR
AUTHOR J.D.BALEJA,B.D.SYKES
REVDAT 5 16-FEB-22 1D19 1 REMARK
REVDAT 4 24-FEB-09 1D19 1 VERSN
REVDAT 3 01-APR-03 1D19 1 JRNL
REVDAT 2 15-OCT-94 1D19 1 COMPND EXPDTA
REVDAT 1 15-JUL-91 1D19 0
JRNL AUTH J.D.BALEJA,M.W.GERMANN,J.H.VAN DE SANDE,B.D.SYKES
JRNL TITL SOLUTION CONFORMATION OF PURINE-PYRIMIDINE DNA OCTAMERS
JRNL TITL 2 USING NUCLEAR MAGNETIC RESONANCE, RESTRAINED MOLECULAR
JRNL TITL 3 DYNAMICS AND NOE-BASED REFINEMENT.
JRNL REF J.MOL.BIOL. V. 215 411 1990
JRNL REFN ISSN 0022-2836
JRNL PMID 2231713
JRNL DOI 10.1016/S0022-2836(05)80361-4
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH J.D.BALEJA,J.MOULT,B.D.SYKES
REMARK 1 TITL DISTANCE MEASUREMENT AND STRUCTURE REFINEMENT WITH NOE DATA
REMARK 1 REF J.MAGN.RESON. V. 87 375 1990
REMARK 1 REFN ISSN 0022-2364
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : GROMOS
REMARK 3 AUTHORS : DE VLIEG ET AL.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS THEN REFINED AGAINST
REMARK 3 PRIMARY NOE DATA. THE R VALUE IS 0.19 OVER ALL OBSERVED,
REMARK 3 QUANTIFIED, NOE CROSSPEAK INTENSITIES. THE NOE-BASED PROCEDURE
REMARK 3 USED TO REFINE THESE STRUCTURES INCLUDED CORRELATION TIME
REMARK 3 ADJUSTMENT FACTORS, WHICH ARE APPROXIMATELY RELATED TO THE
REMARK 3 INVERSE OF THE TEMPERATURE FACTORS ASSOCIATED WITH X-RAY
REMARK 3 CRYSTALLOGRAPHY. THESE VALUES ARE INCLUDED IN THE COLUMN
REMARK 3 NORMALLY USED FOR TEMPERATURE FACTORS. VALUES OF 0.0 APPEAR FOR
REMARK 3 NON-HYDROGEN ATOMS, WHICH WERE NOT USED IN THE NMR CALCULATIONS.
REMARK 3 FURTHER DETAILS ARE GIVEN IN REFERENCE 1.
REMARK 4
REMARK 4 1D19 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000172624.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : NULL
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : NULL
REMARK 210 SPECTROMETER MODEL : NULL
REMARK 210 SPECTROMETER MANUFACTURER : NULL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : ENERGY MINIMIZATION, MOLECULAR
REMARK 210 DYNAMICS
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 : NULL
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: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 DG A 1 C5 DG A 1 N7 -0.062
REMARK 500 DG A 1 N9 DG A 1 C4 -0.050
REMARK 500 DT A 2 C4 DT A 2 C5 -0.057
REMARK 500 DT A 2 C5 DT A 2 C6 0.054
REMARK 500 DT A 2 C5 DT A 2 C7 0.037
REMARK 500 DA A 3 C5 DA A 3 N7 -0.067
REMARK 500 DA A 3 N9 DA A 3 C4 -0.041
REMARK 500 DC A 4 N1 DC A 4 C6 0.038
REMARK 500 DC A 4 C5 DC A 4 C6 0.049
REMARK 500 DG A 5 C5 DG A 5 N7 -0.057
REMARK 500 DT A 6 C5 DT A 6 C6 0.048
REMARK 500 DA A 7 C5 DA A 7 N7 -0.059
REMARK 500 DA A 7 N9 DA A 7 C4 -0.051
REMARK 500 DG B 9 C5 DG B 9 N7 -0.063
REMARK 500 DG B 9 N9 DG B 9 C4 -0.050
REMARK 500 DT B 10 C5 DT B 10 C6 0.042
REMARK 500 DA B 11 C5 DA B 11 N7 -0.059
REMARK 500 DA B 11 N9 DA B 11 C4 -0.041
REMARK 500 DC B 12 C5 DC B 12 C6 0.051
REMARK 500 DG B 13 C5 DG B 13 N7 -0.062
REMARK 500 DG B 13 N9 DG B 13 C4 -0.049
REMARK 500 DT B 14 C5 DT B 14 C6 0.044
REMARK 500 DA B 15 C5 DA B 15 N7 -0.062
REMARK 500 DA B 15 N9 DA B 15 C4 -0.047
REMARK 500 DC B 16 N1 DC B 16 C6 0.037
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 DG A 1 C6 - N1 - C2 ANGL. DEV. = -5.2 DEGREES
REMARK 500 DG A 1 N1 - C2 - N3 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DG A 1 C2 - N3 - C4 ANGL. DEV. = 9.1 DEGREES
REMARK 500 DG A 1 N3 - C4 - C5 ANGL. DEV. = -7.2 DEGREES
REMARK 500 DG A 1 C5 - C6 - N1 ANGL. DEV. = 7.0 DEGREES
REMARK 500 DG A 1 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES
REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = -3.3 DEGREES
REMARK 500 DG A 1 N3 - C4 - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 DG A 1 C5 - C6 - O6 ANGL. DEV. = -7.8 DEGREES
REMARK 500 DT A 2 N1 - C2 - N3 ANGL. DEV. = 5.3 DEGREES
REMARK 500 DT A 2 C2 - N3 - C4 ANGL. DEV. = -6.0 DEGREES
REMARK 500 DT A 2 N3 - C4 - C5 ANGL. DEV. = 4.2 DEGREES
REMARK 500 DT A 2 N3 - C2 - O2 ANGL. DEV. = -3.8 DEGREES
REMARK 500 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES
REMARK 500 DA A 3 N1 - C2 - N3 ANGL. DEV. = -6.9 DEGREES
REMARK 500 DA A 3 C2 - N3 - C4 ANGL. DEV. = 9.0 DEGREES
REMARK 500 DA A 3 N3 - C4 - C5 ANGL. DEV. = -6.9 DEGREES
REMARK 500 DA A 3 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DA A 3 N3 - C4 - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 DG A 5 C6 - N1 - C2 ANGL. DEV. = -5.5 DEGREES
REMARK 500 DG A 5 C2 - N3 - C4 ANGL. DEV. = 8.4 DEGREES
REMARK 500 DG A 5 N3 - C4 - C5 ANGL. DEV. = -7.3 DEGREES
REMARK 500 DG A 5 C5 - C6 - N1 ANGL. DEV. = 7.5 DEGREES
REMARK 500 DG A 5 C4 - C5 - N7 ANGL. DEV. = -3.4 DEGREES
REMARK 500 DG A 5 C5 - N7 - C8 ANGL. DEV. = 3.3 DEGREES
REMARK 500 DG A 5 N7 - C8 - N9 ANGL. DEV. = -3.1 DEGREES
REMARK 500 DG A 5 N3 - C4 - N9 ANGL. DEV. = 5.4 DEGREES
REMARK 500 DG A 5 C5 - C6 - O6 ANGL. DEV. = -8.3 DEGREES
REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DT A 6 N1 - C2 - N3 ANGL. DEV. = 4.6 DEGREES
REMARK 500 DT A 6 C2 - N3 - C4 ANGL. DEV. = -6.3 DEGREES
REMARK 500 DT A 6 N3 - C4 - C5 ANGL. DEV. = 4.9 DEGREES
REMARK 500 DT A 6 N3 - C2 - O2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES
REMARK 500 DA A 7 N1 - C2 - N3 ANGL. DEV. = -6.7 DEGREES
REMARK 500 DA A 7 C2 - N3 - C4 ANGL. DEV. = 8.7 DEGREES
REMARK 500 DA A 7 N3 - C4 - C5 ANGL. DEV. = -7.0 DEGREES
REMARK 500 DA A 7 C5 - N7 - C8 ANGL. DEV. = 3.1 DEGREES
REMARK 500 DA A 7 N7 - C8 - N9 ANGL. DEV. = -3.5 DEGREES
REMARK 500 DA A 7 N3 - C4 - N9 ANGL. DEV. = 5.1 DEGREES
REMARK 500 DG B 9 C6 - N1 - C2 ANGL. DEV. = -5.6 DEGREES
REMARK 500 DG B 9 N1 - C2 - N3 ANGL. DEV. = -3.7 DEGREES
REMARK 500 DG B 9 C2 - N3 - C4 ANGL. DEV. = 9.6 DEGREES
REMARK 500 DG B 9 N3 - C4 - C5 ANGL. DEV. = -8.2 DEGREES
REMARK 500 DG B 9 C5 - C6 - N1 ANGL. DEV. = 7.1 DEGREES
REMARK 500 DG B 9 C4 - C5 - N7 ANGL. DEV. = -3.5 DEGREES
REMARK 500 DG B 9 C5 - N7 - C8 ANGL. DEV. = 3.4 DEGREES
REMARK 500 DG B 9 N3 - C4 - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 DG B 9 C5 - C6 - O6 ANGL. DEV. = -7.9 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 80 ANGLE DEVIATIONS.
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 DG A 1 0.08 SIDE CHAIN
REMARK 500 DT A 2 0.09 SIDE CHAIN
REMARK 500 DA A 3 0.05 SIDE CHAIN
REMARK 500 DC A 4 0.08 SIDE CHAIN
REMARK 500 DG A 5 0.10 SIDE CHAIN
REMARK 500 DT A 6 0.10 SIDE CHAIN
REMARK 500 DG B 9 0.09 SIDE CHAIN
REMARK 500 DT B 10 0.11 SIDE CHAIN
REMARK 500 DC B 12 0.08 SIDE CHAIN
REMARK 500 DG B 13 0.10 SIDE CHAIN
REMARK 500 DT B 14 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1D18 RELATED DB: PDB
DBREF 1D19 A 1 8 PDB 1D19 1D19 1 8
DBREF 1D19 B 9 16 PDB 1D19 1D19 9 16
SEQRES 1 A 8 DG DT DA DC DG DT DA DC
SEQRES 1 B 8 DG DT DA DC DG DT DA DC
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
Complete list - 16 202 Bytes