Header list of 1k9h.pdb file
Complete list - 23 202 Bytes
HEADER DNA 29-OCT-01 1K9H
TITLE NMR STRUCTURE OF DNA TGTGAGCGCTCACA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3';
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES;
COMPND 5 OTHER_DETAILS: THIS SEQUENCE HAS BEEN DERIVED FROM THE NATURAL LAC
COMPND 6 OPERATOR SEQUENCE BY SYMMETRIZING THE MINIMUM REQUIRED LENGTH FOR LAC
COMPND 7 REPRESSOR BINDING.
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS LAC OPERATOR, DOUBLE HELIX, DNA
EXPDTA SOLUTION NMR
AUTHOR K.KALUARACHCHI,D.G.GORENSTEIN,B.A.LUXON
REVDAT 3 23-FEB-22 1K9H 1 REMARK
REVDAT 2 24-FEB-09 1K9H 1 VERSN
REVDAT 1 07-NOV-01 1K9H 0
JRNL AUTH K.KALUARACHCHI,D.G.GORENSTEIN,B.A.LUXON
JRNL TITL HOW DO PROTEINS RECOGNIZE DNA? SOLUTION STRUCTURE AND LOCAL
JRNL TITL 2 CONFORMATIONAL DYNAMICS OF LAC OPERATORS BY 2D NMR
JRNL REF J.BIOMOL.STRUCT.DYN. V.N 11 123 2000
JRNL REFN ISSN 0739-1102
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER VERSIONS 3-5, MORASS 1.0
REMARK 3 AUTHORS : KOLLMAN. P. (AMBER), MEADOWS. R.P. (MORASS)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1K9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-01.
REMARK 100 THE DEPOSITION ID IS D_1000014727.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.4
REMARK 210 IONIC STRENGTH : 150 MM KCL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 3.6 MM OLIGONUCLEOTIDE, 55 MM
REMARK 210 POTASSIUM PHOSPHATE, 150 MM KCL,
REMARK 210 0.1MM NAN3
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : VXRS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX
REMARK 210 RELAXATION, SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 2
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE WITH
REMARK 210 EXPERIMENTAL NOESY SPECTRUM,
REMARK 210 STRUCTURES WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD HOMONUCLEAR
REMARK 210 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 DT A 1 O5' DT A 1 C5' -0.371
REMARK 500 DT A 1 O4' DT A 1 C4' -0.071
REMARK 500 DT A 1 O3' DT A 1 C3' -0.041
REMARK 500 DT A 3 O4' DT A 3 C4' -0.063
REMARK 500 DC A 9 P DC A 9 OP1 -0.132
REMARK 500 DC A 9 P DC A 9 O5' -0.125
REMARK 500 DC A 9 O4' DC A 9 C4' -0.062
REMARK 500 DT B 15 O4' DT B 15 C4' -0.068
REMARK 500 DT B 24 O4' DT B 24 C4' -0.060
REMARK 500 DA B 28 O3' DA B 28 C3' -0.050
REMARK 500 DA B 28 C4 DA B 28 C5 -0.046
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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES
REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES
REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES
REMARK 500 DG A 6 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES
REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES
REMARK 500 DC A 9 P - O5' - C5' ANGL. DEV. = 15.0 DEGREES
REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 DT A 10 C4' - C3' - C2' ANGL. DEV. = -4.2 DEGREES
REMARK 500 DT A 10 C3' - C2' - C1' ANGL. DEV. = 7.9 DEGREES
REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DA A 12 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 DA A 12 C4' - C3' - C2' ANGL. DEV. = -9.9 DEGREES
REMARK 500 DA A 12 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DA A 12 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 DC A 13 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES
REMARK 500 DA A 14 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DT B 15 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES
REMARK 500 DG B 18 O4' - C1' - N9 ANGL. DEV. = 7.6 DEGREES
REMARK 500 DG B 18 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES
REMARK 500 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES
REMARK 500 DT B 24 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES
REMARK 500 DT B 24 C4' - C3' - C2' ANGL. DEV. = -4.9 DEGREES
REMARK 500 DT B 24 C3' - C2' - C1' ANGL. DEV. = 8.0 DEGREES
REMARK 500 DC B 25 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 DC B 27 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 DA B 28 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES
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 4 0.08 SIDE CHAIN
REMARK 500 DA A 5 0.08 SIDE CHAIN
REMARK 500 DC A 7 0.07 SIDE CHAIN
REMARK 500 DA A 12 0.09 SIDE CHAIN
REMARK 500 DT B 15 0.09 SIDE CHAIN
REMARK 500 DG B 16 0.07 SIDE CHAIN
REMARK 500 DG B 18 0.10 SIDE CHAIN
REMARK 500 DA B 19 0.06 SIDE CHAIN
REMARK 500 DC B 25 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1K9L RELATED DB: PDB
REMARK 900 1K9L IS THE SOLUTION STRUCTURE OF THE DNA OLIGOMER TATGAGCGCTCATA.
DBREF 1K9H A 1 14 PDB 1K9H 1K9H 1 14
DBREF 1K9H B 15 28 PDB 1K9H 1K9H 15 28
SEQRES 1 A 14 DT DG DT DG DA DG DC DG DC DT DC DA DC
SEQRES 2 A 14 DA
SEQRES 1 B 14 DT DG DT DG DA DG DC DG DC DT DC DA DC
SEQRES 2 B 14 DA
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 - 23 202 Bytes