HEADER DNA, RNA 07-DEC-10 2L7D TITLE RIBONUCLEOTIDE PERTURBATION OF DNA STRUCTURE: SOLUTION STRUCTURE OF TITLE 2 [D(CGC)R(G)D(AATTCGCG)]2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*CP*GP*C)-R(P*G)-D(P*AP*AP*TP*TP*CP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RG4 SUBSTITUTED DREW DICKERSON DODECAMER SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS RIBONUCLEOTIDE SUBSTITUTED DNA, DNA, RNA EXPDTA SOLUTION NMR NUMMDL 5 AUTHOR E.F.DEROSE,L.PERERA,M.S.MURRAY,T.A.KUNKEL,R.E.LONDON REVDAT 3 01-MAY-24 2L7D 1 REMARK REVDAT 2 13-JUN-12 2L7D 1 JRNL VERSN REVDAT 1 01-JUN-11 2L7D 0 JRNL AUTH E.F.DEROSE,L.PERERA,M.S.MURRAY,T.A.KUNKEL,R.E.LONDON JRNL TITL SOLUTION STRUCTURE OF THE DICKERSON DNA DODECAMER CONTAINING JRNL TITL 2 A SINGLE RIBONUCLEOTIDE. JRNL REF BIOCHEMISTRY V. 51 2407 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22390730 JRNL DOI 10.1021/BI201710Q REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ 2.1B, XPLOR-NIH 2.25 REMARK 3 AUTHORS : VARIAN (VNMRJ), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000102048. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.0 MM RG4 SUBSTITUTED DREW REMARK 210 DICKERSON DODECAMER, 50.0 MM REMARK 210 SODIUM CHLORIDE, 50.0 MM SODIUM REMARK 210 PHOSPHATE, 0.5 MM EDTA, 100% D2O; REMARK 210 2.0 MM RG4 SUBSTITUTED DREW REMARK 210 DICKERSON DODECAMER, 50.0 MM REMARK 210 SODIUM CHLORIDE, 50.0 MM SODIUM REMARK 210 PHOSPHATE, 0.5 MM EDTA, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-1H COSY; 2D 1H-31P COSY; REMARK 210 2D 1H-31P J-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2010.190.16.149, NMRVIEW REMARK 210 8.0.B64, XPLOR-NIH 2.25 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 5 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 1 DC A 9 C4' DC A 9 C3' 0.065 REMARK 500 1 DC B 21 C4' DC B 21 C3' 0.066 REMARK 500 2 DC A 9 C4' DC A 9 C3' 0.061 REMARK 500 2 DC B 21 C4' DC B 21 C3' 0.062 REMARK 500 3 DC A 9 C4' DC A 9 C3' 0.062 REMARK 500 3 DC B 21 C4' DC B 21 C3' 0.063 REMARK 500 5 DC A 9 C4' DC A 9 C3' 0.065 REMARK 500 5 DC B 21 C4' DC B 21 C3' 0.064 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 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 DC A 1 C4' - C3' - C2' ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 DC B 13 C4' - C3' - C2' ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 7 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 3 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 4 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DT A 8 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DT B 19 C6 - C5 - C7 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 DT B 20 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17351 RELATED DB: BMRB DBREF 2L7D A 1 12 PDB 2L7D 2L7D 1 12 DBREF 2L7D B 13 24 PDB 2L7D 2L7D 13 24 SEQRES 1 A 12 DC DG DC G DA DA DT DT DC DG DC DG SEQRES 1 B 12 DC DG DC G DA DA DT DT DC DG 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