HEADER DNA 13-DEC-03 1RVI TITLE SOLUTION STRUCTURE OF THE DNA DODECAMER CGTTTTAAAACG COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*TP*TP*TP*TP*AP*AP*AP*AP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DOUBLE HELIX, DNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR R.STEFL,H.WU,S.RAVINDRANATHAN,V.SKLENAR,J.FEIGON REVDAT 3 02-MAR-22 1RVI 1 REMARK REVDAT 2 24-FEB-09 1RVI 1 VERSN REVDAT 1 10-FEB-04 1RVI 0 JRNL AUTH R.STEFL,H.WU,S.RAVINDRANATHAN,V.SKLENAR,J.FEIGON JRNL TITL DNA A-TRACT BENDING IN THREE DIMENSIONS: SOLVING THE DA4T4 JRNL TITL 2 VS. DT4A4 CONUNDRUM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 1177 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 14739342 JRNL DOI 10.1073/PNAS.0308143100 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, D.A., ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 833 RESTRAINTS, 549 ARE NOE-DERIVED DISTANCE RESTRAINTS, 160 REMARK 3 TORSION ANGLE RESTRAINTS, 24 PSEUDOROTATION PHASE ANGLE REMARK 3 RESTRAINTS, 24 DISTANCE RESTRAINTS FROM W-C HYDROGEN BONDS, AND REMARK 3 72 RESIDUAL DIPOLAR COUPLINGS. REMARK 4 REMARK 4 1RVI COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000021068. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 288 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 25 MM NH4CL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM (IN DUPLEX) CGTTTTAAAACG, REMARK 210 25MM NH4CL, 100% D2O OR 90% H2O/ REMARK 210 10% D2O; 2MM (IN DUPLEX) REMARK 210 CGTTTTAAAACG, U-13C,15N, 25MM REMARK 210 NH4CL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; DQF-COSY; 31P REMARK 210 SPIN-ECHO DIFF CT-HSQC; SPIN- REMARK 210 ECHO DIFF CH-HCCH; HSQC (WITH REMARK 210 AND WITHOUT PF1 PHAGE) REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, FOR DETAILS REMARK 210 SEE (PADRTA ET AL. (2002) J. REMARK 210 BIOMOL. NMR 24, 1-24) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING RESIDUAL DIPOLAR REMARK 210 COUPLINGS 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 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 1 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT A 3 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 DA A 7 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA A 7 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 8 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DA A 8 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DA A 9 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA A 9 C5 - C6 - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA A 10 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA A 10 C5 - C6 - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC A 11 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC A 11 N1 - C2 - O2 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DC A 11 N3 - C2 - O2 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 12 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DC B 13 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DT B 15 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT B 17 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT B 18 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DA B 19 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 DA B 19 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DA B 20 C4 - C5 - C6 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DA B 20 C5 - C6 - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DA B 20 N1 - C6 - N6 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DA B 21 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DA B 21 C5 - C6 - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DA B 22 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DA B 22 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 DC B 23 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 23 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 DC B 23 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 DG B 24 N1 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DC A 1 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 3 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DT A 4 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DT A 5 C6 - C5 - C7 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 DA A 7 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 DA A 7 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 DA A 7 N1 - C6 - N6 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DA A 8 C4 - C5 - C6 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 361 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 DT A 4 0.08 SIDE CHAIN REMARK 500 1 DT A 6 0.09 SIDE CHAIN REMARK 500 1 DT B 16 0.09 SIDE CHAIN REMARK 500 1 DT B 18 0.09 SIDE CHAIN REMARK 500 2 DT A 4 0.08 SIDE CHAIN REMARK 500 2 DT A 6 0.13 SIDE CHAIN REMARK 500 2 DT B 16 0.07 SIDE CHAIN REMARK 500 2 DT B 18 0.10 SIDE CHAIN REMARK 500 3 DT A 4 0.07 SIDE CHAIN REMARK 500 3 DT A 6 0.09 SIDE CHAIN REMARK 500 3 DC A 11 0.09 SIDE CHAIN REMARK 500 3 DT B 16 0.09 SIDE CHAIN REMARK 500 3 DT B 18 0.10 SIDE CHAIN REMARK 500 4 DT A 4 0.09 SIDE CHAIN REMARK 500 4 DT A 6 0.09 SIDE CHAIN REMARK 500 4 DT B 16 0.10 SIDE CHAIN REMARK 500 4 DT B 18 0.09 SIDE CHAIN REMARK 500 5 DT A 4 0.08 SIDE CHAIN REMARK 500 5 DT A 6 0.10 SIDE CHAIN REMARK 500 5 DA A 10 0.08 SIDE CHAIN REMARK 500 5 DC A 11 0.07 SIDE CHAIN REMARK 500 5 DT B 16 0.10 SIDE CHAIN REMARK 500 5 DT B 18 0.11 SIDE CHAIN REMARK 500 6 DT A 4 0.07 SIDE CHAIN REMARK 500 6 DT A 6 0.12 SIDE CHAIN REMARK 500 6 DA A 10 0.06 SIDE CHAIN REMARK 500 6 DT B 16 0.06 SIDE CHAIN REMARK 500 6 DT B 18 0.10 SIDE CHAIN REMARK 500 6 DA B 20 0.06 SIDE CHAIN REMARK 500 6 DA B 22 0.07 SIDE CHAIN REMARK 500 7 DT A 4 0.08 SIDE CHAIN REMARK 500 7 DT A 6 0.12 SIDE CHAIN REMARK 500 7 DT B 16 0.08 SIDE CHAIN REMARK 500 7 DT B 18 0.10 SIDE CHAIN REMARK 500 8 DT A 4 0.07 SIDE CHAIN REMARK 500 8 DT A 6 0.12 SIDE CHAIN REMARK 500 8 DA A 10 0.07 SIDE CHAIN REMARK 500 8 DT B 16 0.07 SIDE CHAIN REMARK 500 8 DT B 18 0.11 SIDE CHAIN REMARK 500 8 DC B 23 0.08 SIDE CHAIN REMARK 500 9 DT A 4 0.08 SIDE CHAIN REMARK 500 9 DT A 6 0.12 SIDE CHAIN REMARK 500 9 DC A 11 0.07 SIDE CHAIN REMARK 500 9 DT B 16 0.09 SIDE CHAIN REMARK 500 9 DT B 18 0.09 SIDE CHAIN REMARK 500 9 DA B 21 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RVH RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE DNA DODECAMER GCAAAATTTTGC. DBREF 1RVI A 1 12 PDB 1RVI 1RVI 1 12 DBREF 1RVI B 13 24 PDB 1RVI 1RVI 13 24 SEQRES 1 A 12 DC DG DT DT DT DT DA DA DA DA DC DG SEQRES 1 B 12 DC DG DT DT DT DT DA DA DA DA DC DG 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