HEADER DNA 24-MAR-11 2RRQ TITLE DNA OLIGOMER CONTAINING PROPYLENE CROSS-LINKED CYCLIC 2'- TITLE 2 DEOXYURIDYLATE DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*CP*TP*TP*CP*AP*(JDT)P*TP*AP*CP*AP*TP*CP*C)- COMPND 3 3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (5'-D(*GP*GP*AP*TP*GP*TP*AP*AP*TP*GP*AP*AP*GP*G)-3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA, NUCLEIC ACID, DEOXYURIDYLATE, BENT DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.FURUITA,S.MURATA,J.G.JEE,S.ICHIKAWA,A.MATSUDA,C.KOJIMA REVDAT 1 08-JUN-11 2RRQ 0 JRNL AUTH K.FURUITA,S.MURATA,J.G.JEE,S.ICHIKAWA,A.MATSUDA,C.KOJIMA JRNL TITL STRUCTURAL FEATURE OF BENT DNA RECOGNIZED BY HMGB1 JRNL REF J.AM.CHEM.SOC. V. 133 5788 2011 JRNL REFN ISSN 0002-7863 JRNL PMID 21443191 JRNL DOI 10.1021/JA2013399 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RRQ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-11. REMARK 100 THE RCSB ID CODE IS RCSB150207. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 303 REMARK 210 PH : 6.8; 6.8 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : NULL; NULL REMARK 210 SAMPLE CONTENTS : 50MM SODIUM PHOSPHATE-1, 100MM REMARK 210 SODIUM CHLORIDE-2, 0.5MM REMARK 210 PROPYLENE-DNA-3, 0.5MM PROPYLENE- REMARK 210 DNA-4, 90% H2O/10% D2O; 50MM REMARK 210 SODIUM PHOSPHATE-5, 100MM SODIUM REMARK 210 CHLORIDE-6, 0.5MM PROPYLENE-DNA- REMARK 210 7, 0.5MM PROPYLENE-DNA-8, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D DQF-COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.2, NMRPIPE, SPARKY, REMARK 210 MARDIGRAS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2 DC A 14 H22 DG B 15 1.51 REMARK 500 O2 DC A 5 H22 DG B 24 1.51 REMARK 500 O2 DC A 2 H22 DG B 27 1.52 REMARK 500 O2 DC A 13 H22 DG B 16 1.54 REMARK 500 O2 DC A 10 H22 DG B 19 1.55 REMARK 500 O2 DC A 1 H22 DG B 28 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 11437 RELATED DB: BMRB REMARK 900 RELATED ID: 2RRR RELATED DB: PDB DBREF 2RRQ A 1 14 PDB 2RRQ 2RRQ 1 14 DBREF 2RRQ B 15 28 PDB 2RRQ 2RRQ 15 28 SEQRES 1 A 14 DC DC DT DT DC DA JDT DT DA DC DA DT DC SEQRES 2 A 14 DC SEQRES 1 B 14 DG DG DA DT DG DT DA DA DT DG DA DA DG SEQRES 2 B 14 DG MODRES 2RRQ JDT A 7 DT HET JDT A 7 34 HETNAM JDT 2'-DEOXY-5-ETHYLURIDINE 5'-(DIHYDROGEN PHOSPHATE) FORMUL 1 JDT C11 H17 N2 O8 P LINK O3' DA A 6 P JDT A 7 1555 1555 1.61 LINK O3' JDT A 7 P DT A 8 1555 1555 1.61 LINK C72 JDT A 7 C7 DT A 8 1555 1555 1.50 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 91 0 1 0 0 0 0 6 0 0 0 4 END