HEADER RNA 03-JAN-02 1KPZ TITLE PEMV-1 P1-P2 FRAMESHIFTING PSEUDOKNOT REGULARIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: P1-P2 FRAMESHIFTING PSEUDOKNOT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PEA ENATION MOSAIC VIRUS TYPE I RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: NATURALLY OCCURING SEQUENCE OF THE P1-P2 SOURCE 4 FRAMESHIFTING PSEUDOKNOT FROM PEA ENATION MOSAIC VIRUS TYPE I. IN SOURCE 5 VITRO SP6 TRANSCRIPTION. KEYWDS PSEUDOKNOT, FRAMESHIFTING, LUTEOVIRUS, TRIPLE HELIX, PROTONATED KEYWDS 2 CYTIDINE, RIBONUCLEIC ACID, RNA EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE AUTHOR P.L.NIXON,D.P.GIEDROC REVDAT 4 24-JAN-18 1KPZ 1 JRNL REMARK REVDAT 3 24-FEB-09 1KPZ 1 VERSN REVDAT 2 18-MAR-03 1KPZ 1 JRNL REMARK MASTER REVDAT 1 11-JAN-02 1KPZ 0 JRNL AUTH P.L.NIXON,A.RANGAN,Y.-G.KIM,A.RICH,D.W.HOFFMAN,M.HENNIG, JRNL AUTH 2 D.P.GIEDROC JRNL TITL SOLUTION STRUCTURE OF A LUTEOVIRAL P1-P2 FRAMESHIFTING MRNA JRNL TITL 2 PSEUDOKNOT JRNL REF J.MOL.BIOL. V. 322 621 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12225754 JRNL DOI 10.1016/S0022-2836(02)00779-9 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER, A.T REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KPZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015214. 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 : 100 MM KCL, 5 MM MGCL2; 100 MM REMARK 210 KCL, 5 MM MGCL2 REMARK 210 PRESSURE : ATMOSPHERIC ATM; ATMOSPHERIC ATM REMARK 210 SAMPLE CONTENTS : 2 MM PEMV-1 RNA REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.851 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 RES C SSSEQI REMARK 465 G A 0 REMARK 465 A A 1 REMARK 465 A A 2 REMARK 465 U A 3 REMARK 465 A A 32 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 C A 16 H61 A A 25 1.42 REMARK 500 HO2' A A 27 O4' G A 28 1.53 REMARK 500 O2' C A 6 O2' A A 22 2.15 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 U A 4 C2' U A 4 C1' -0.106 REMARK 500 C A 5 C2' C A 5 C1' -0.111 REMARK 500 G A 7 C2' G A 7 C1' -0.130 REMARK 500 G A 8 C2' G A 8 C1' -0.142 REMARK 500 G A 11 C2' G A 11 C1' -0.128 REMARK 500 A A 12 C2' A A 12 C1' -0.130 REMARK 500 C A 15 C2' C A 15 C1' -0.123 REMARK 500 C A 16 C2' C A 16 C1' -0.097 REMARK 500 G A 17 C2' G A 17 C1' -0.136 REMARK 500 G A 18 C5' G A 18 C4' -0.045 REMARK 500 G A 18 C2' G A 18 C1' -0.101 REMARK 500 A A 19 C2' A A 19 C1' -0.148 REMARK 500 A A 19 C8 A A 19 N9 -0.049 REMARK 500 A A 21 C2 A A 21 N3 -0.096 REMARK 500 A A 21 N3 A A 21 C4 -0.061 REMARK 500 A A 21 C4 A A 21 C5 -0.061 REMARK 500 A A 21 C8 A A 21 N9 -0.059 REMARK 500 A A 21 N9 A A 21 C4 -0.072 REMARK 500 C A 24 N1 C A 24 C6 0.046 REMARK 500 G A 28 C2' G A 28 C1' -0.132 REMARK 500 U A 29 C2' U A 29 C1' -0.068 REMARK 500 C A 30 C2' C A 30 C1' -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 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 5 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 C A 5 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C A 5 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 C A 6 C1' - O4' - C4' ANGL. DEV. = -4.7 DEGREES REMARK 500 C A 6 C4' - C3' - C2' ANGL. DEV. = -6.9 DEGREES REMARK 500 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 G A 7 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 G A 7 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -3.9 DEGREES REMARK 500 G A 8 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 8 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 U A 9 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 G A 11 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 G A 11 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 11 C8 - N9 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 A A 12 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 12 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 A A 12 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 13 C3' - C2' - C1' ANGL. DEV. = 5.1 DEGREES REMARK 500 U A 14 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 C A 15 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 G A 17 C5' - C4' - O4' ANGL. DEV. = -8.3 DEGREES REMARK 500 G A 17 O4' - C1' - N9 ANGL. DEV. = 9.0 DEGREES REMARK 500 G A 17 N7 - C8 - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 G A 17 C8 - N9 - C4 ANGL. DEV. = -4.2 DEGREES REMARK 500 G A 18 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 G A 18 N7 - C8 - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 G A 18 C8 - N9 - C4 ANGL. DEV. = -5.2 DEGREES REMARK 500 A A 19 C5' - C4' - O4' ANGL. DEV. = -11.1 DEGREES REMARK 500 A A 19 O4' - C1' - N9 ANGL. DEV. = 9.2 DEGREES REMARK 500 A A 19 N7 - C8 - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 A A 19 C8 - N9 - C4 ANGL. DEV. = -4.8 DEGREES REMARK 500 G A 20 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 G A 20 C8 - N9 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 A A 21 N3 - C4 - C5 ANGL. DEV. = 4.7 DEGREES REMARK 500 A A 21 C5 - N7 - C8 ANGL. DEV. = -4.7 DEGREES REMARK 500 A A 21 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 A A 21 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES REMARK 500 A A 21 N9 - C4 - C5 ANGL. DEV. = 3.6 DEGREES REMARK 500 A A 21 N3 - C4 - N9 ANGL. DEV. = -8.3 DEGREES REMARK 500 A A 22 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 A A 22 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 A A 22 C8 - N9 - C4 ANGL. DEV. = -3.2 DEGREES REMARK 500 A A 23 N7 - C8 - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 C A 24 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 A A 25 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 A A 25 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 62 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 U A 4 0.12 SIDE CHAIN REMARK 500 C A 5 0.10 SIDE CHAIN REMARK 500 C A 6 0.09 SIDE CHAIN REMARK 500 G A 7 0.09 SIDE CHAIN REMARK 500 G A 8 0.12 SIDE CHAIN REMARK 500 U A 9 0.11 SIDE CHAIN REMARK 500 G A 11 0.08 SIDE CHAIN REMARK 500 A A 12 0.10 SIDE CHAIN REMARK 500 C A 15 0.10 SIDE CHAIN REMARK 500 C A 16 0.10 SIDE CHAIN REMARK 500 G A 17 0.09 SIDE CHAIN REMARK 500 G A 18 0.11 SIDE CHAIN REMARK 500 A A 19 0.08 SIDE CHAIN REMARK 500 A A 21 0.21 SIDE CHAIN REMARK 500 A A 22 0.14 SIDE CHAIN REMARK 500 A A 25 0.06 SIDE CHAIN REMARK 500 A A 26 0.06 SIDE CHAIN REMARK 500 G A 28 0.09 SIDE CHAIN REMARK 500 U A 29 0.10 SIDE CHAIN REMARK 500 C A 30 0.17 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KPY RELATED DB: PDB REMARK 900 PEMV-1 STRUCTURAL ENSEMBLE DBREF 1KPZ A 0 32 PDB 1KPZ 1KPZ 0 32 SEQRES 1 A 33 G A A U U C C G G U CH G A SEQRES 2 A 33 C U C C G G A G A A A C A SEQRES 3 A 33 A A G U C A A MODRES 1KPZ 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 1.61 LINK O3' CH A 10 P G A 11 1555 1555 1.65 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