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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10