HEADER DNA 23-MAR-09 2KH0 TITLE 2-HYDROXY-7-NITROFLUORENE COVALENTLY LINKED INTO A 13MER DNA TITLE 2 DUPLEX - SOLUTION STRUCTURE OF THE FACE-DOWN ORIENTATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*TP*GP*CP*AP*(3DR)P*AP*CP*GP*TP*CP*G)- COMPND 3 3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*CP*GP*AP*CP*GP*TP*(3DR)P*TP*GP*CP*AP*GP*C)- COMPND 8 3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA, SOLUTION STRUCTURE, BASE PAIR MIMIC, CONFORMATIONAL KEYWDS 2 FLEXIBILITY EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR A.DALLMANN,M.PFAFFE,C.MUEGGE,R.MAHRWALD,S.A.KOVALENKO, AUTHOR 2 N.P.ERNSTING REVDAT 1 01-DEC-09 2KH0 0 JRNL AUTH A.DALLMANN,M.PFAFFE,R.MAHRWALD,S.A.KOVALENKO, JRNL AUTH 2 N.P.ERNSTING JRNL TITL LOCAL THZ TIME DOMAIN SPECTROSCOPY OF DUPLEX DNA JRNL TITL 2 VIA FLUORESCENCE OF AN EMBEDDED PROBE JRNL REF J.PHYS.CHEM.B V. 113 15619 2009 JRNL REFN ISSN 1089-5647 JRNL PMID 19764701 JRNL DOI 10.1021/JP906037G REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH 2.20 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KH0 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-09. REMARK 100 THE RCSB ID CODE IS RCSB101109. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3 MM STRAND I-1, 3 MM STRAND REMARK 210 II-2, 20 MG/ML PF1 PHAGE-3, 10 REMARK 210 MM SODIUM PHOSPHATE-4, 150 MM REMARK 210 SODIUM CHLORIDE-5, 100% D2O; 3 REMARK 210 MM STRAND I-6, 3 MM STRAND II- REMARK 210 7, 10 MM SODIUM PHOSPHATE-8, REMARK 210 150 MM SODIUM CHLORIDE-9, 100% REMARK 210 D2O; 3 MM STRAND I-10, 3 MM REMARK 210 STRAND II-11, 10 MM SODIUM REMARK 210 PHOSPHATE-12, 150 MM SODIUM REMARK 210 CHLORIDE-13, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H COSY; 2D 1H-1H REMARK 210 NOESY; 2D 1H-13C HSQC; 2D 1H- REMARK 210 13C HSQC_DECOUPLED; 2D 1H-1H REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : GIFA 4, X-PLOR_NIH 2.20, X- REMARK 210 PLOR_NIH 2.21, CARA 1.8.4, REMARK 210 TOPSPIN 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 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 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 H22 DG A 10 O2 DC B 17 1.60 REMARK 500 H22 DG A 4 O2 DC B 23 1.60 REMARK 500 H22 DG A 1 O2 DC B 26 1.60 REMARK 500 O2 DC A 2 H22 DG B 25 1.60 REMARK 500 O2 DC A 5 H22 DG B 22 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 1 3DR B 20 38.4 D L WRONG HAND REMARK 500 2 3DR B 20 38.4 D L WRONG HAND REMARK 500 3 3DR B 20 38.6 D L WRONG HAND REMARK 500 4 3DR B 20 38.1 D L WRONG HAND REMARK 500 5 3DR B 20 38.4 D L WRONG HAND REMARK 500 6 3DR B 20 38.2 D L WRONG HAND REMARK 500 7 3DR B 20 38.1 D L WRONG HAND REMARK 500 8 3DR B 20 38.1 D L WRONG HAND REMARK 500 9 3DR B 20 38.2 D L WRONG HAND REMARK 500 10 3DR B 20 38.3 D L WRONG HAND REMARK 500 11 3DR B 20 38.2 D L WRONG HAND REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HNF A 27 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KGZ RELATED DB: PDB REMARK 900 RELATED ID: 2KH1 RELATED DB: PDB DBREF 2KH0 A 1 13 PDB 2KH0 2KH0 1 13 DBREF 2KH0 B 14 26 PDB 2KH0 2KH0 14 26 SEQRES 1 A 13 DG DC DT DG DC DA 3DR DA DC DG DT DC DG SEQRES 1 B 13 DC DG DA DC DG DT 3DR DT DG DC DA DG DC HET 3DR A 7 18 HET 3DR B 20 19 HET HNF A 27 25 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM HNF 7-NITRO-9H-FLUOREN-2-OL HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN HNF 2-HYDROXY-7-NITROFLUORENE FORMUL 1 3DR 2(C5 H11 O6 P) FORMUL 3 HNF C13 H9 N O3 LINK O3' DA A 6 P 3DR A 7 1555 1555 1.61 LINK O3' 3DR A 7 P DA A 8 1555 1555 1.61 LINK O3' DT B 19 P 3DR B 20 1555 1555 1.61 LINK O3' 3DR B 20 P DT B 21 1555 1555 1.61 LINK C1' 3DR A 7 O1 HNF A 27 1555 1555 1.42 SITE 1 AC1 6 DA A 6 3DR A 7 DA A 8 DT B 19 SITE 2 AC1 6 3DR B 20 DT B 21 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 MASTER 113 0 3 0 0 0 2 6 0 0 0 2 END