10 20 30 40 50 60 70 80 1D0U - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 14-SEP-99 1D0U
TITLE SOLUTION STRUCTURE OF AN RNA BINDING SITE FOR PHAGE MS2 TITLE 2 COAT PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHAGE MS2 RNA BINDING SITE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: MS2 REPLICASE OPERATOR HAIRPIN
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: TRANSCRIPTION BY T7 RNA PLOYMERASE
KEYWDS RNA HAIRPIN, BULGED BASE, STEM-LOOP
EXPDTA SOLUTION NMR
NUMMDL 23
MDLTYP MINIMIZED AVERAGE
AUTHOR J.S.SMITH,E.P.NIKONOWICZ
REVDAT 2 24-FEB-09 1D0U 1 VERSN REVDAT 1 24-MAY-00 1D0U 0
JRNL AUTH J.S.SMITH,E.P.NIKONOWICZ JRNL TITL PHOSPHOROTHIOATE SUBSTITUTION CAN SUBSTANTIALLY JRNL TITL 2 ALTER RNA CONFORMATION. JRNL REF BIOCHEMISTRY V. 39 5642 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10801314 JRNL DOI 10.1021/BI992712B
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE CALCULATED USING 469 REMARK 3 CONFORMATIONALLY RESTRICTIVE NOE DISTANCE CONSTRAINTS (I.E., REMARK 3 INTRA-RESIDUE SUGAR-SUGAR NOES ARE NOT INCLUDED), 20 H-BOND REMARK 3 BASE PAIR CONSTRAINTS, 30 BACKBONE DIHEDRAL RESTRAINTS, AND REMARK 3 DIHEDRAL RESTRAINTS TO RESTRICT SUGAR PUCKER CONFORMATION.
REMARK 4 REMARK 4 1D0U COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-99. REMARK 100 THE RCSB ID CODE IS RCSB009693.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : ~50 MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.2 MM REPLICASE OPERATOR RNA REMARK 210 U-15N,13C; 10 MM KPI BUFFER; REMARK 210 10 MM NACL; 0.2 MM EDTA; 2.2 REMARK 210 MM REPLICASE OPERATOR RNA U- REMARK 210 15N,13C; 10 MM KPI BUFFER; 10 REMARK 210 MM NACL; 0.2 MM EDTA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 2D REMARK 210 NOESY, 3D_13C-SEPARATED_NOESY, REMARK 210 DQF-COSY, 31P-1H HETCOR REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 1994, FELIX 1997, X- REMARK 210 PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING AND REMARK 210 MOLECULAR DYNAMICS REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 111 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH REMARK 210 ACCEPTABLE COVALENT GEOMETRY, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1/2 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND 2D/3D HETERONUCLEAR TECHNIQUES
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. = 4.6 DEGREES REMARK 500 1 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 2 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 A A 17 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 G A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 3 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 3 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 3 A A 4 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 7 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 10 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 G A 14 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 G A 14 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 3 G A 15 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 3 G A 16 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 3 G A 16 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 389 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D0T RELATED DB: PDB REMARK 900 PHOSPHOROTHIOATE SUBSTITUTED PHAGE MS2 REPLICASE OPERATOR REMARK 900 RNA HAIRPIN.
DBREF 1D0U A 1 21 PDB 1D0U 1D0U 1 21
SEQRES 1 A 21 G G G A U C A C C A U U A SEQRES 2 A 21 G G G A U C U C
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