10 20 30 40 50 60 70 80 2RP1 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 25-APR-08 2RP1
TITLE REFINED SOLUTION STRUCTURE OF THE PEMV-1 MRNA PSEUDOKNOT, TITLE 2 REGULARIZED AVERAGE STRUCTURE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEMV-1 MRNA PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: RNA WAS PRODUCED BY IN VITRO TRANSCRIPTION SOURCE 4 USING SP6 RNA POLYMERASE
KEYWDS RNA PSEUDOKNOT, FRAMESHIFTING
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR P.V.CORNISH,M.HENNIG,D.P.GIEDROC
REVDAT 1 31-MAR-09 2RP1 0
JRNL AUTH D.P.GIEDROC,P.V.CORNISH JRNL TITL FRAMESHIFTING RNA PSEUDOKNOTS: STRUCTURE AND JRNL TITL 2 MECHANISM. JRNL REF VIRUS RES. V. 139 193 2009 JRNL REFN ISSN 0168-1702 JRNL PMID 18621088 JRNL DOI 10.1016/J.VIRUSRES.2008.06.008
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR_NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2RP1 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-MAY-08. REMARK 100 THE RCSB ID CODE IS RCSB150112.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2 MM RNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 0.1 MM DSS, 5 MM REMARK 210 MAGNESIUM CHLORIDE, 90% H2O/ REMARK 210 10% D2O; 2 MM [U-100% 13C; U- REMARK 210 100% 15N] RNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 0.1 MM DSS, 5 MM REMARK 210 MAGNESIUM CHLORIDE, 100% D2O; REMARK 210 2 MM [U-100% 13C; U-100% 15N] REMARK 210 RNA, 10 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 0.1 MM DSS, 20 MG/ML REMARK 210 PF1 PHAGE, 5 MM MAGNESIUM REMARK 210 CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY, 2D 1H-1H REMARK 210 NOESY, J-MODULATED CT-HSQC, CT REMARK 210 -TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ, 800 MHZ, 500 MHZ, REMARK 210 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER, VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, NMRPIPE, FELIX REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 28 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 O2' G A 7 O5' G A 8 1.90 REMARK 500 O2' A A 21 O3' A A 22 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 C A 16 O5' C A 16 C5' -0.076 REMARK 500 A A 19 C4' A A 19 C3' -0.063 REMARK 500 A A 19 O3' A A 19 C3' -0.090 REMARK 500 G A 20 P G A 20 O5' -0.123 REMARK 500 G A 20 O5' G A 20 C5' -0.085 REMARK 500 G A 20 C5' G A 20 C4' -0.079 REMARK 500 G A 20 C3' G A 20 C2' -0.082 REMARK 500 G A 20 O3' G A 20 C3' -0.125 REMARK 500 G A 20 C1' G A 20 N9 -0.191 REMARK 500 G A 20 C2 G A 20 N3 -0.053 REMARK 500 G A 20 C5 G A 20 N7 0.045 REMARK 500 G A 20 C8 G A 20 N9 -0.043 REMARK 500 G A 20 N9 G A 20 C4 -0.161 REMARK 500 A A 19 O3' G A 20 P -0.089 REMARK 500 A A 21 P A A 21 O5' -0.071 REMARK 500 A A 21 O5' A A 21 C5' -0.114 REMARK 500 G A 20 O3' A A 21 P -0.191 REMARK 500 A A 22 P A A 22 O5' -0.063 REMARK 500 A A 26 C3' A A 26 C2' -0.076 REMARK 500 A A 27 O5' A A 27 C5' -0.069 REMARK 500 REMARK 500 REMARK: NULL 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 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 G A 8 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 8 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 G A 11 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 11 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 A A 12 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 12 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 12 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 C A 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 15 C5' - C4' - O4' ANGL. DEV. = 5.9 DEGREES REMARK 500 C A 16 C5' - C4' - C3' ANGL. DEV. = -11.3 DEGREES REMARK 500 G A 17 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 G A 17 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 G A 18 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 A A 19 C5' - C4' - O4' ANGL. DEV. = 5.5 DEGREES REMARK 500 A A 19 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 A A 19 N7 - C8 - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 G A 20 P - O5' - C5' ANGL. DEV. = -10.0 DEGREES REMARK 500 G A 20 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 G A 20 C5' - C4' - O4' ANGL. DEV. = 6.8 DEGREES REMARK 500 G A 20 C1' - O4' - C4' ANGL. DEV. = -5.9 DEGREES REMARK 500 G A 20 C2' - C3' - O3' ANGL. DEV. = -14.1 DEGREES REMARK 500 G A 20 C4' - C3' - C2' ANGL. DEV. = 7.2 DEGREES REMARK 500 G A 20 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 G A 20 O4' - C1' - C2' ANGL. DEV. = 5.7 DEGREES REMARK 500 G A 20 N9 - C1' - C2' ANGL. DEV. = -11.7 DEGREES REMARK 500 G A 20 N3 - C4 - C5 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 20 C5 - N7 - C8 ANGL. DEV. = -5.1 DEGREES REMARK 500 G A 20 C8 - N9 - C4 ANGL. DEV. = 4.0 DEGREES REMARK 500 G A 20 N3 - C4 - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 G A 20 C4 - N9 - C1' ANGL. DEV. = -10.8 DEGREES REMARK 500 A A 21 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 A A 21 O3' - P - O5' ANGL. DEV. = -14.2 DEGREES REMARK 500 A A 23 O5' - P - OP2 ANGL. DEV. = -6.9 DEGREES REMARK 500 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 26 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 A A 27 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 A A 27 O3' - P - O5' ANGL. DEV. = -13.8 DEGREES REMARK 500 G A 28 C5 - N7 - C8 ANGL. DEV. = -3.1 DEGREES REMARK 500 G A 28 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 28 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 U A 29 O5' - C5' - C4' ANGL. DEV. = -10.2 DEGREES REMARK 500 C A 30 O5' - P - OP2 ANGL. DEV. = -6.2 DEGREES REMARK 500 C A 30 O5' - C5' - C4' ANGL. DEV. = -8.6 DEGREES REMARK 500 C A 30 O3' - P - O5' ANGL. DEV. = -13.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G A 8 0.05 SIDE_CHAIN REMARK 500 G A 11 0.07 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KPY RELATED DB: PDB REMARK 900 PREVIOUS LOWER RESOLUTION STRUCTURE REMARK 900 RELATED ID: 1KPZ RELATED DB: PDB REMARK 900 PREVIOUS LOWER RESOLUTION STRUCTURE REMARK 900 RELATED ID: 2RP0 RELATED DB: PDB
DBREF 2RP1 A 4 30 PDB 2RP1 2RP1 4 30
SEQRES 1 A 27 U C C G G U CH G A C U C C SEQRES 2 A 27 G G A G A A A C A A A G U SEQRES 3 A 27 C
MODRES 2RP1 CH A 10 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
HET CH A 10 32
HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE
FORMUL 1 CH C9 H15 N3 O8 P 1+
LINK O3' U A 9 P CH A 10 1555 1555 1.60 LINK O3' CH A 10 P G A 11 1555 1555 1.59
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