HEADER RNA 18-JUL-09 2RQJ TITLE QUADRUPLEX STRUCTURE OF AN RNA APTAMER AGAINST BOVINE PRION PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*GP*AP*GP*GP*AP*GP*GP*AP*GP*GP*A)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS APTAMER, PRION, QUADRUPLEX, RNA EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR M.KATAHIRA,T.MASHIMA,A.MATSUGAMI,F.NISHIKAWA,S.NISHIKAWA REVDAT 3 29-MAY-24 2RQJ 1 REMARK REVDAT 2 16-MAR-22 2RQJ 1 REMARK REVDAT 1 17-NOV-09 2RQJ 0 JRNL AUTH T.MASHIMA,A.MATSUGAMI,F.NISHIKAWA,S.NISHIKAWA,M.KATAHIRA JRNL TITL UNIQUE QUADRUPLEX STRUCTURE AND INTERACTION OF AN RNA JRNL TITL 2 APTAMER AGAINST BOVINE PRION PROTEIN JRNL REF NUCLEIC ACIDS RES. V. 37 6249 2009 JRNL REFN ISSN 0305-1048 JRNL PMID 19666719 JRNL DOI 10.1093/NAR/GKP647 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.20, X-PLOR NIH 2.20 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RQJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-AUG-09. REMARK 100 THE DEPOSITION ID IS D_1000150165. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 303 REMARK 210 PH : 6.2; 6.2 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1MM RNA-1, 10MM POTASSIUM REMARK 210 PHOSPHATE-2, 100MM POTASSIUM REMARK 210 CHLORIDE-3, 0.01MM DSS-4, 3MM REMARK 210 SODIUM AZIDE-5, 95% H2O/5% D2O; REMARK 210 1MM RNA-6, 10MM POTASSIUM REMARK 210 PHOSPHATE-7, 100MM POTASSIUM REMARK 210 CHLORIDE-8, 0.01MM DSS-9, 3MM REMARK 210 SODIUM AZIDE-10, 95% H2O/5% 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 JRHMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, TOPSPIN, SPARKY, REMARK 210 NMRPIPE, PIPP REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 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: 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 HO2' G A 1 O5' G A 2 1.54 REMARK 500 N7 G A 1 H21 G A 10 1.59 REMARK 500 N7 G B 13 H21 G B 22 1.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 2RQJ A 1 12 PDB 2RQJ 2RQJ 1 12 DBREF 2RQJ B 13 24 PDB 2RQJ 2RQJ 13 24 SEQRES 1 A 12 G G A G G A G G A G G A SEQRES 1 B 12 G G A G G A G G A G G A 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