HEADER RNA 15-AUG-05 2AP0 TITLE SOLUTION STRUCTURE OF THE C27A SCYLV P1-P2 FRAMESHIFTING PSEUDOKNOT, TITLE 2 20 LOWEST ENERGY STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: C27A SUGARCANE YELLOW LEAF VIRUS RNA PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: MUTANT OF NATURALLY OCCURING RNA FRAGMENT THAT FORMS SOURCE 4 AN RNA PSEUDOKNOT IN SUGARCANE YELLOW LEAF VIRUS KEYWDS RNA PSEUDOKNOT; FRAMESHIFTING, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.V.CORNISH,D.P.GIEDROC REVDAT 5 09-MAR-22 2AP0 1 REMARK LINK REVDAT 4 24-FEB-09 2AP0 1 VERSN REVDAT 3 28-NOV-06 2AP0 1 JRNL REVDAT 2 10-OCT-06 2AP0 1 JRNL REVDAT 1 05-SEP-06 2AP0 0 JRNL AUTH P.V.CORNISH,S.N.STAMMLER,D.P.GIEDROC JRNL TITL THE GLOBAL STRUCTURES OF A WILD-TYPE AND POORLY FUNCTIONAL JRNL TITL 2 PLANT LUTEOVIRAL MRNA PSEUDOKNOT ARE ESSENTIALLY IDENTICAL JRNL REF RNA V. 12 1959 2006 JRNL REFN ISSN 1355-8382 JRNL PMID 17000902 JRNL DOI 10.1261/RNA.199006 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE MAC OS X VERSION, XPLOR-NIH 2.10 REMARK 3 AUTHORS : F. DELAGLIO, S. GRZESIEK, G. W. VUISTER, G. ZHU, REMARK 3 J. PFEIFER AND A. BAX (NMRPIPE), G. MARIUS CLORE , REMARK 3 JOHN KUSZEWSKI, CHARLES D. SCHWIETERS, AND NICO REMARK 3 TJANDRA (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AP0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034149. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 283; 298 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 100MM KCL, 5MM MGCL2; 100MM KCL, REMARK 210 5MM MGCL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2.7MM C27A SCYLV; 100MM KCL; 5MM REMARK 210 MGCL2; 2.7MM C27A SCYLV; 100MM REMARK 210 KCL; 5MM MGCL2; 2.7MM C27A SCYLV; REMARK 210 100MM KCL; 5MM MGCL2; 15 MG/ML REMARK 210 PF1 PHAGE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; TROSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3 REMARK 210 METHOD USED : SIMULATED ANNEALING STARTING REMARK 210 WITH RANDOM COORDINATES FOLLOWED REMARK 210 BY REFINEMENT WITH RESIDUAL REMARK 210 DIPOLAR COUPLINGS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 H22 G A 6 H61 A A 23 1.35 REMARK 500 O2' A A 20 H5'' A A 21 1.49 REMARK 500 H2' G A 4 O4' U A 5 1.52 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 1 C A 14 C2' C A 14 C1' -0.053 REMARK 500 1 C A 15 C2' C A 15 C1' -0.048 REMARK 500 1 U A 18 C2' U A 18 C1' -0.080 REMARK 500 2 G A 7 C2' G A 7 C1' -0.076 REMARK 500 2 C A 14 C2' C A 14 C1' -0.052 REMARK 500 2 U A 18 C2' U A 18 C1' -0.087 REMARK 500 3 G A 7 C2' G A 7 C1' -0.059 REMARK 500 3 G A 7 O3' G A 7 C3' 0.074 REMARK 500 3 C A 10 C2' C A 10 C1' -0.050 REMARK 500 3 G A 12 N7 G A 12 C8 -0.042 REMARK 500 3 C A 14 C2' C A 14 C1' -0.100 REMARK 500 3 C A 15 C2' C A 15 C1' -0.057 REMARK 500 3 U A 18 C2' U A 18 C1' -0.101 REMARK 500 4 G A 4 C2' G A 4 C1' -0.048 REMARK 500 4 C A 14 C2' C A 14 C1' -0.052 REMARK 500 4 U A 18 C2' U A 18 C1' -0.076 REMARK 500 4 U A 19 C2' U A 19 C1' -0.092 REMARK 500 4 U A 19 O4' U A 19 C4' -0.082 REMARK 500 4 U A 19 N1 U A 19 C6 -0.056 REMARK 500 5 G A 4 C2' G A 4 C1' -0.064 REMARK 500 5 U A 5 C2' U A 5 C1' -0.107 REMARK 500 5 G A 6 C5' G A 6 C4' 0.099 REMARK 500 5 G A 6 C2' G A 6 C1' -0.063 REMARK 500 5 G A 6 O4' G A 6 C1' 0.075 REMARK 500 5 G A 6 C2 G A 6 N3 0.050 REMARK 500 5 G A 6 C5 G A 6 N7 -0.037 REMARK 500 5 G A 6 N7 G A 6 C8 -0.036 REMARK 500 5 G A 6 C8 G A 6 N9 -0.068 REMARK 500 5 G A 6 N9 G A 6 C4 0.051 REMARK 500 5 C A 14 C2' C A 14 C1' -0.099 REMARK 500 5 C A 15 C5' C A 15 C4' 0.082 REMARK 500 5 U A 18 C2' U A 18 C1' -0.099 REMARK 500 6 C A 14 C2' C A 14 C1' -0.057 REMARK 500 6 U A 18 C2' U A 18 C1' -0.097 REMARK 500 7 C A 14 C2' C A 14 C1' -0.058 REMARK 500 7 C A 15 C2' C A 15 C1' -0.054 REMARK 500 7 U A 18 C2' U A 18 C1' -0.098 REMARK 500 7 U A 19 C5' U A 19 C4' 0.082 REMARK 500 8 G A 4 C2' G A 4 C1' -0.077 REMARK 500 8 U A 5 C5' U A 5 C4' 0.077 REMARK 500 8 C A 14 C2' C A 14 C1' -0.052 REMARK 500 8 U A 18 C2' U A 18 C1' -0.105 REMARK 500 9 C A 10 C2' C A 10 C1' -0.049 REMARK 500 9 C A 14 C2' C A 14 C1' -0.104 REMARK 500 9 C A 15 C2' C A 15 C1' -0.049 REMARK 500 9 A A 16 C2' A A 16 C1' -0.048 REMARK 500 9 U A 18 C2' U A 18 C1' -0.096 REMARK 500 10 G A 7 C2' G A 7 C1' -0.071 REMARK 500 10 G A 12 N7 G A 12 C8 -0.036 REMARK 500 10 C A 14 C2' C A 14 C1' -0.049 REMARK 500 REMARK 500 THIS ENTRY HAS 109 BOND DEVIATIONS. 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 1 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 4 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G A 6 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 7 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 12 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 12 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 16 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 U A 19 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 A A 20 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 20 C8 - N9 - C4 ANGL. DEV. = -2.9 DEGREES REMARK 500 1 A A 21 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 1 A A 21 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 A A 21 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 21 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 22 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 A A 23 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 24 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 A A 24 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 1 A A 26 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 A A 27 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 A A 27 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 G A 29 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 G A 29 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 G A 30 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 G A 30 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 2 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A A 3 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 2 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 4 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 G A 6 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 G A 6 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 G A 6 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 G A 7 O4' - C1' - N9 ANGL. DEV. = 9.9 DEGREES REMARK 500 2 G A 7 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 G A 9 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 G A 9 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 2 G A 12 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 G A 12 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 A A 13 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 794 ANGLE DEVIATIONS. 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 1 A A 3 0.07 SIDE CHAIN REMARK 500 1 G A 4 0.08 SIDE CHAIN REMARK 500 1 G A 6 0.08 SIDE CHAIN REMARK 500 1 G A 7 0.06 SIDE CHAIN REMARK 500 1 C A 10 0.07 SIDE CHAIN REMARK 500 1 C A 11 0.07 SIDE CHAIN REMARK 500 1 G A 12 0.08 SIDE CHAIN REMARK 500 1 C A 14 0.07 SIDE CHAIN REMARK 500 1 C A 15 0.08 SIDE CHAIN REMARK 500 1 A A 16 0.09 SIDE CHAIN REMARK 500 1 C A 17 0.07 SIDE CHAIN REMARK 500 1 U A 18 0.11 SIDE CHAIN REMARK 500 1 G A 29 0.07 SIDE CHAIN REMARK 500 1 G A 30 0.08 SIDE CHAIN REMARK 500 2 A A 3 0.07 SIDE CHAIN REMARK 500 2 G A 4 0.08 SIDE CHAIN REMARK 500 2 U A 5 0.07 SIDE CHAIN REMARK 500 2 G A 6 0.07 SIDE CHAIN REMARK 500 2 G A 7 0.06 SIDE CHAIN REMARK 500 2 C A 10 0.06 SIDE CHAIN REMARK 500 2 C A 11 0.08 SIDE CHAIN REMARK 500 2 G A 12 0.07 SIDE CHAIN REMARK 500 2 C A 14 0.06 SIDE CHAIN REMARK 500 2 C A 15 0.08 SIDE CHAIN REMARK 500 2 A A 16 0.09 SIDE CHAIN REMARK 500 2 C A 17 0.08 SIDE CHAIN REMARK 500 2 U A 18 0.11 SIDE CHAIN REMARK 500 2 A A 26 0.05 SIDE CHAIN REMARK 500 2 C A 28 0.07 SIDE CHAIN REMARK 500 2 G A 29 0.08 SIDE CHAIN REMARK 500 2 G A 30 0.07 SIDE CHAIN REMARK 500 3 A A 3 0.07 SIDE CHAIN REMARK 500 3 G A 4 0.08 SIDE CHAIN REMARK 500 3 U A 5 0.07 SIDE CHAIN REMARK 500 3 G A 6 0.07 SIDE CHAIN REMARK 500 3 G A 7 0.06 SIDE CHAIN REMARK 500 3 C A 10 0.07 SIDE CHAIN REMARK 500 3 C A 11 0.08 SIDE CHAIN REMARK 500 3 G A 12 0.07 SIDE CHAIN REMARK 500 3 C A 14 0.06 SIDE CHAIN REMARK 500 3 C A 15 0.08 SIDE CHAIN REMARK 500 3 A A 16 0.09 SIDE CHAIN REMARK 500 3 C A 17 0.07 SIDE CHAIN REMARK 500 3 U A 18 0.08 SIDE CHAIN REMARK 500 3 G A 29 0.08 SIDE CHAIN REMARK 500 3 G A 30 0.08 SIDE CHAIN REMARK 500 4 A A 3 0.07 SIDE CHAIN REMARK 500 4 G A 4 0.08 SIDE CHAIN REMARK 500 4 U A 5 0.08 SIDE CHAIN REMARK 500 4 G A 6 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 311 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AP5 RELATED DB: PDB REMARK 900 AVERAGE STRUCTURE DBREF 2AP0 A 3 30 PDB 2AP0 2AP0 3 30 SEQRES 1 A 28 A G U G G CH G C C G A C C SEQRES 2 A 28 A C U U A A A A A C A A C SEQRES 3 A 28 G G MODRES 2AP0 CH A 8 C N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE HET CH A 8 32 HETNAM CH N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE FORMUL 1 CH C9 H15 N3 O8 P 1+ LINK O3' G A 7 P CH A 8 1555 1555 1.61 LINK O3' CH A 8 P G A 9 1555 1555 1.61 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