10 20 30 40 50 60 70 80 1K9H - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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)- COMPND 3 3'; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THIS SEQUENCE HAS BEEN DERIVED FROM THE COMPND 7 NATURAL LAC OPERATOR SEQUENCE BY SYMMETRIZING THE MINIMUM COMPND 8 REQUIRED LENGTH FOR LAC 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 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 JRNL TITL 2 AND LOCAL CONFORMATIONAL DYNAMICS OF LAC OPERATORS JRNL TITL 3 BY 2D NMR JRNL REF J.BIOMOL.STRUCT.DYN. V.CONV 123 2000 JRNL REFN ISSN 0739-1102
REMARK 1
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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-01. REMARK 100 THE RCSB ID CODE IS RCSB014727.
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 REMARK 210 KCL, 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 REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 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 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. = -4.3 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 REMARK 900 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