Header list of 1cqo.pdb file
Complete list - 16 20 Bytes
HEADER DNA 09-AUG-99 1CQO
TITLE NMR STRUCTURE OF THE PALINDROMIC DNA DECAMER D(GCGTTAACGC)2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*TP*TP*AP*AP*CP*GP*C)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS SEQUENCE IS THE HPA1 RESTRICTION SITE.
KEYWDS DOUBLE HELIX, B-DNA, RESTRICTION SITE, HPA 1, DNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR J.A.SMITH,V.T.TSUI,W.J.CHAZIN,D.A.CASE
REVDAT 3 16-FEB-22 1CQO 1 REMARK
REVDAT 2 24-FEB-09 1CQO 1 VERSN
REVDAT 1 23-AUG-99 1CQO 0
JRNL AUTH J.A.SMITH,V.T.TSUI,W.J.CHAZIN,D.A.CASE
JRNL TITL NMR STRUCTURE OF THE PALINDROMIC DNA DECAMER D(GCGTTAACGC)2
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : FELIX 95, AMBER 5.0
REMARK 3 AUTHORS : MOLECULAR SIMULATIONS, INC. (FELIX), PEARLMAN, ET.
REMARK 3 AL. (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: DIRECT RELAXATION MATRIX REFINEMENT
REMARK 3 WITH EXPLICIT SOLVENT. DETAILS IN PRIMARY CITATION.
REMARK 4
REMARK 4 1CQO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-99.
REMARK 100 THE DEPOSITION ID IS D_1000009493.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300
REMARK 210 PH : 7
REMARK 210 IONIC STRENGTH : 50MM NACL, 20MM NAPO4
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2MM D(GCGTTAACGC); 20MM NA3PO4,
REMARK 210 50MM NACL, 0.1% NAN3.; 2MM
REMARK 210 D(GCGTTAACGC); 20MM NA3PO4, 50MM
REMARK 210 NACL, 0.1% NAN3.
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : DOUBLE-QUANTUM; DQF-COSY; E
REMARK 210 -COSY; 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NAB 2.1, AMBER 5.0
REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS.
REMARK 210 RELAXATION MATRIX REFINEMENT.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 10
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES
REMARK 210 SUBMITTED
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES.
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 2 DG B 19 C5' DG B 19 C4' 0.044
REMARK 500 8 DG B 19 C5' DG B 19 C4' 0.045
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 2 O4' - C4' - C3' ANGL. DEV. = 4.0 DEGREES
REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DT A 5 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 DT A 5 C4 - C5 - C7 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -7.0 DEGREES
REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 1 DG B 11 O5' - C5' - C4' ANGL. DEV. = 18.9 DEGREES
REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 DT B 14 C4 - C5 - C7 ANGL. DEV. = 4.8 DEGREES
REMARK 500 1 DT B 14 C6 - C5 - C7 ANGL. DEV. = -7.1 DEGREES
REMARK 500 1 DT B 15 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DT B 15 C4 - C5 - C7 ANGL. DEV. = 5.9 DEGREES
REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -8.1 DEGREES
REMARK 500 1 DA B 16 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES
REMARK 500 1 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 1 DG B 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 1 DC B 20 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DG A 1 C5' - C4' - O4' ANGL. DEV. = 8.6 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 2 DC A 2 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES
REMARK 500 2 DG A 3 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DT A 4 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -6.4 DEGREES
REMARK 500 2 DT A 5 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -6.1 DEGREES
REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES
REMARK 500 2 DG A 9 O4' - C1' - C2' ANGL. DEV. = -4.8 DEGREES
REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 2 DG B 11 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 2 DG B 11 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES
REMARK 500 2 DG B 11 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES
REMARK 500 2 DC B 12 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 DG B 13 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DT B 14 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 DT B 14 C4 - C5 - C7 ANGL. DEV. = 4.0 DEGREES
REMARK 500 2 DT B 14 C6 - C5 - C7 ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DT B 15 C4 - C5 - C7 ANGL. DEV. = 5.6 DEGREES
REMARK 500 2 DT B 15 C6 - C5 - C7 ANGL. DEV. = -7.6 DEGREES
REMARK 500 2 DA B 16 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DA B 17 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES
REMARK 500 2 DG B 19 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES
REMARK 500 3 DG A 1 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES
REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 3 DC A 2 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES
REMARK 500 3 DG A 3 C5' - C4' - O4' ANGL. DEV. = 7.8 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 236 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 1 DC A 2 0.08 SIDE CHAIN
REMARK 500 1 DC A 8 0.14 SIDE CHAIN
REMARK 500 1 DG B 11 0.10 SIDE CHAIN
REMARK 500 1 DG B 13 0.06 SIDE CHAIN
REMARK 500 1 DA B 17 0.07 SIDE CHAIN
REMARK 500 1 DC B 18 0.06 SIDE CHAIN
REMARK 500 1 DC B 20 0.06 SIDE CHAIN
REMARK 500 2 DG A 1 0.06 SIDE CHAIN
REMARK 500 2 DC A 8 0.09 SIDE CHAIN
REMARK 500 2 DG B 11 0.07 SIDE CHAIN
REMARK 500 2 DC B 18 0.08 SIDE CHAIN
REMARK 500 2 DG B 19 0.12 SIDE CHAIN
REMARK 500 3 DC A 2 0.07 SIDE CHAIN
REMARK 500 3 DC A 8 0.08 SIDE CHAIN
REMARK 500 3 DC B 18 0.08 SIDE CHAIN
REMARK 500 3 DG B 19 0.10 SIDE CHAIN
REMARK 500 4 DG A 1 0.09 SIDE CHAIN
REMARK 500 4 DG A 3 0.08 SIDE CHAIN
REMARK 500 4 DT A 4 0.08 SIDE CHAIN
REMARK 500 4 DC A 8 0.11 SIDE CHAIN
REMARK 500 4 DG A 9 0.07 SIDE CHAIN
REMARK 500 4 DG B 11 0.06 SIDE CHAIN
REMARK 500 4 DG B 13 0.06 SIDE CHAIN
REMARK 500 4 DT B 15 0.06 SIDE CHAIN
REMARK 500 4 DA B 17 0.07 SIDE CHAIN
REMARK 500 4 DC B 18 0.14 SIDE CHAIN
REMARK 500 4 DG B 19 0.09 SIDE CHAIN
REMARK 500 5 DA A 7 0.05 SIDE CHAIN
REMARK 500 5 DC A 8 0.07 SIDE CHAIN
REMARK 500 5 DG B 11 0.05 SIDE CHAIN
REMARK 500 5 DG B 19 0.06 SIDE CHAIN
REMARK 500 5 DC B 20 0.07 SIDE CHAIN
REMARK 500 6 DG A 1 0.07 SIDE CHAIN
REMARK 500 6 DC A 2 0.06 SIDE CHAIN
REMARK 500 6 DG A 3 0.07 SIDE CHAIN
REMARK 500 6 DC A 8 0.12 SIDE CHAIN
REMARK 500 6 DG B 11 0.07 SIDE CHAIN
REMARK 500 6 DA B 17 0.07 SIDE CHAIN
REMARK 500 6 DC B 18 0.07 SIDE CHAIN
REMARK 500 7 DG A 1 0.10 SIDE CHAIN
REMARK 500 7 DC A 2 0.07 SIDE CHAIN
REMARK 500 7 DA A 6 0.07 SIDE CHAIN
REMARK 500 7 DC A 8 0.09 SIDE CHAIN
REMARK 500 7 DG A 9 0.06 SIDE CHAIN
REMARK 500 7 DC A 10 0.06 SIDE CHAIN
REMARK 500 7 DA B 17 0.10 SIDE CHAIN
REMARK 500 7 DC B 18 0.11 SIDE CHAIN
REMARK 500 7 DC B 20 0.06 SIDE CHAIN
REMARK 500 8 DG A 1 0.06 SIDE CHAIN
REMARK 500 8 DC A 8 0.07 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 65 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 132D RELATED DB: PDB
REMARK 900 132D CONTAINS THE SAME CENTRAL 8 BASEPAIR SEQUENCE.
REMARK 900 RELATED ID: 194D RELATED DB: PDB
REMARK 900 194D CONTAINS THIS SEQUENCE AS ITS 10 CENTRAL BASEPAIRS.
REMARK 900 RELATED ID: 195D RELATED DB: PDB
REMARK 900 195D CONTAINS THIS SEQUENCE IN COMPLEX WITH NETROPSIN.
DBREF 1CQO A 1 10 PDB 1CQO 1CQO 1 10
DBREF 1CQO B 11 20 PDB 1CQO 1CQO 11 20
SEQRES 1 A 10 DG DC DG DT DT DA DA DC DG DC
SEQRES 1 B 10 DG DC DG DT DT DA DA DC DG 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
MODEL 1
Complete list - 16 20 Bytes