10 20 30 40 50 60 70 80 1HOQ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA, RNA 11-DEC-00 1HOQ
TITLE CHIMERIC RNA/DNA HAIRPIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-R(*GP*GP*AP*C)- COMPND 3 D(P*TP*TP*CP*GP*GP*TP*CP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SOLID PHASE SYNTHESIS, PHOSPHORAMIDITE SOURCE 4 CHEMISTRY
KEYWDS HAIRPIN, DNA, RNA
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.Y.DENISOV,K.GEHRING
REVDAT 3 24-FEB-09 1HOQ 1 VERSN REVDAT 2 01-APR-03 1HOQ 1 JRNL REVDAT 1 07-NOV-01 1HOQ 0
JRNL AUTH A.Y.DENISOV,A.M.NORONHA,C.J.WILDS,J.F.TREMPE, JRNL AUTH 2 R.T.PON,K.GEHRING,M.J.DAMHA JRNL TITL SOLUTION STRUCTURE OF AN ARABINONUCLEIC ACID JRNL TITL 2 (ANA)/RNA DUPLEX IN A CHIMERIC HAIRPIN: COMPARISON JRNL TITL 3 WITH 2'-FLUORO-ANA/RNA AND DNA/RNA HYBRIDS. JRNL REF NUCLEIC ACIDS RES. V. 29 4284 2001 JRNL REFN ISSN 0305-1048 JRNL PMID 11691916 JRNL DOI 10.1093/NAR/29.21.4284
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.J.DAMHA,A.M.NORONHA,C.J.WILDS,J.F.TREMPE, REMARK 1 AUTH 2 A.Y.DENISOV,R.T.PON,K.GEHRING REMARK 1 TITL PROPERTIES OF ARABINONUCLEIC ACIDS (ANA & REMARK 1 TITL 2 2'F-ANA): IMPLICATIONS FOR THE DESIGN OF ANTISENSE REMARK 1 TITL 3 THERAPEUTICS THAT INVOKE RNASE H CLEAVAGE OF RNA REMARK 1 REF NUCLEOSIDES NUCLEOTIDES V. 20 429 2001 REMARK 1 REF 2 NUCLEIC ACIDS REMARK 1 REFN ISSN 1525-7770 REMARK 1 DOI 10.1081/NCN-100002317
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE REFINED BY NMR- REMARK 3 RESTRAINED MOLECULAR DYNAMICS (14 PS, 300-1000 K) WITH FINAL REMARK 3 ENERGY MINIMIZATION
REMARK 4 REMARK 4 1HOQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-DEC-00. REMARK 100 THE RCSB ID CODE IS RCSB012485.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1ATM REMARK 210 SAMPLE CONTENTS : 1MM HAIRPIN; 1MM HAIRPIN REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY, 2D-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CALCULATED STRUCTURES REMARK 210 SUBMITTED REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMO- REMARK 210 AND HETERONUCLEAR TECHNIQUES: 2D-NOESY, DQF-COSY, TOCSY, H,C- REMARK 210 HMQC, H,P-HETCOSY
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: 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 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DC A 7 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 2 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 DT A 5 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 DC A 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DG A 8 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 DG A 8 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DG A 8 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DG A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DG A 9 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 3 DT A 10 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 3 DC A 11 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 3 DC A 12 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 4 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 G A 2 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 4 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 154 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HO6 RELATED DB: PDB REMARK 900 1HO6 CONTAINS THE SAME HAIRPIN BUT WITH ANA/RNA STEM REMARK 900 RELATED ID: 1FC8 RELATED DB: PDB REMARK 900 1FC8 CONTAINS THE SAME HAIRPIN BUT WITH 2'F-ANA/RNA STEM
DBREF 1HOQ A 1 12 PDB 1HOQ 1HOQ 1 12
SEQRES 1 A 12 G G A C DT DT DC DG DG DT DC DC
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