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