HEADER RNA 26-AUG-01 1JUR TITLE SOLUTION STRUCTURE OF HELIX III IN XENOPUS OOCYTE 5S RRNA. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*CP*UP*GP*AP*GP*GP*AP*GP*AP*CP*UP*CP*AP*GP*AP COMPND 3 *AP*GP*CP*C)-3'; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HELIX III DOMAIN OF XENOPUS OOCYTE 5 S RRNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THE STEM OF THIS HAIRPIN OCCURS NATURALLY IN XENOPUS SOURCE 4 OOCYTES. KEYWDS RNA, 5 S RRNA, BULGE EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR P.W.HUBER,J.P.RIFE,P.B.MOORE REVDAT 3 23-FEB-22 1JUR 1 REMARK REVDAT 2 24-FEB-09 1JUR 1 VERSN REVDAT 1 16-JAN-02 1JUR 0 JRNL AUTH P.W.HUBER,J.P.RIFE,P.B.MOORE JRNL TITL THE STRUCTURE OF HELIX III IN XENOPUS OOCYTE 5 S RRNA: AN JRNL TITL 2 RNA STEM CONTAINING A TWO-NUCLEOTIDE BULGE. JRNL REF J.MOL.BIOL. V. 312 823 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11575935 JRNL DOI 10.1006/JMBI.2001.4966 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR, X-PLOR 3.851 REMARK 3 AUTHORS : VARIAN (VNMR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN ADDITION TO THE EXPERIMENTALLY REMARK 3 DERIVED DISTANCE CONSTRAINTS AND DIHEDRAL ANGLE CONSTRAINTS, THE REMARK 3 STRUCTURES WERE COMPUTED USING 22 NON-EXPERIMENTAL CONSTRAINTS REMARK 3 TO ENSURE WATSON-CRICK BASE PAIRING AND TETRALOOP FORMATION. REMARK 4 REMARK 4 1JUR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014205. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 10; 30 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 100 MM KCL; 100 MM KCL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM HELIX III HAIRPIN; 5MM REMARK 210 CACODYLATE BUFFER (PH 6.5); 100 REMARK 210 MM KCL; 2MM HELIX III HAIRPIN; REMARK 210 5MM CACODYLATE BUFFER (PH 6.5); REMARK 210 100 MM KCL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; REMARK 210 2D_13C_SEPARATED_HMQC; 2D_31P_ REMARK 210 SEPARATED_COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS; INOVA; OMEGA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; GE REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : FELIX 95, X-PLOR 3.851 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH FAVORABLE NON-BOND ENERGY, REMARK 210 STRUCTURES WITH THE LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR 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 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: 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 A A 16 C8 A A 16 N9 -0.056 REMARK 500 2 A A 16 C8 A A 16 N9 -0.055 REMARK 500 3 A A 16 C8 A A 16 N9 -0.056 REMARK 500 4 A A 16 C8 A A 16 N9 -0.055 REMARK 500 5 A A 16 C8 A A 16 N9 -0.057 REMARK 500 6 A A 16 C8 A A 16 N9 -0.056 REMARK 500 7 A A 16 C8 A A 16 N9 -0.054 REMARK 500 8 A A 16 C8 A A 16 N9 -0.055 REMARK 500 9 A A 16 C8 A A 16 N9 -0.051 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 12 C3' - C2' - C1' ANGL. DEV. = -9.5 DEGREES REMARK 500 1 A A 12 N9 - C1' - C2' ANGL. DEV. = 7.8 DEGREES REMARK 500 1 A A 16 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 A A 18 C3' - O3' - P ANGL. DEV. = 9.2 DEGREES REMARK 500 1 A A 19 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 A A 12 C3' - C2' - C1' ANGL. DEV. = -9.3 DEGREES REMARK 500 2 C A 13 C6 - N1 - C2 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 A A 16 O4' - C1' - N9 ANGL. DEV. = 8.4 DEGREES REMARK 500 2 G A 17 C5' - C4' - O4' ANGL. DEV. = 6.5 DEGREES REMARK 500 3 C A 3 C2' - C3' - O3' ANGL. DEV. = 10.9 DEGREES REMARK 500 3 A A 12 C2' - C3' - O3' ANGL. DEV. = 10.9 DEGREES REMARK 500 3 A A 12 C3' - C2' - C1' ANGL. DEV. = -9.0 DEGREES REMARK 500 3 A A 12 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 3 C A 13 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 3 A A 16 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 3 G A 17 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 A A 10 C2' - C3' - O3' ANGL. DEV. = 9.8 DEGREES REMARK 500 4 A A 12 C3' - C2' - C1' ANGL. DEV. = -9.4 DEGREES REMARK 500 4 A A 16 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES REMARK 500 5 A A 12 C3' - C2' - C1' ANGL. DEV. = -9.0 DEGREES REMARK 500 5 A A 12 N9 - C1' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 5 C A 13 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 5 A A 16 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 5 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 A A 18 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 A A 19 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 6 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 A A 12 C3' - C2' - C1' ANGL. DEV. = -9.5 DEGREES REMARK 500 6 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 C A 13 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 6 A A 16 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 6 A A 16 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 A A 12 C2' - C3' - O3' ANGL. DEV. = 9.7 DEGREES REMARK 500 7 A A 12 C3' - C2' - C1' ANGL. DEV. = -8.9 DEGREES REMARK 500 7 C A 13 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 A A 16 O4' - C1' - N9 ANGL. DEV. = 7.8 DEGREES REMARK 500 8 G A 1 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 8 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 8 A A 12 C3' - C2' - C1' ANGL. DEV. = -8.2 DEGREES REMARK 500 8 A A 12 N9 - C1' - C2' ANGL. DEV. = 8.0 DEGREES REMARK 500 8 C A 13 C6 - N1 - C2 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 A A 16 O4' - C1' - N9 ANGL. DEV. = 8.4 DEGREES REMARK 500 8 G A 17 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 9 G A 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 9 C A 4 C6 - N1 - C2 ANGL. DEV. = -2.5 DEGREES REMARK 500 9 A A 12 C2' - C3' - O3' ANGL. DEV. = 9.7 DEGREES REMARK 500 9 A A 12 C3' - C2' - C1' ANGL. DEV. = -8.4 DEGREES REMARK 500 9 A A 12 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 9 U A 14 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 9 A A 16 O4' - C1' - N9 ANGL. DEV. = 7.3 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 1 G A 1 0.08 SIDE CHAIN REMARK 500 1 C A 3 0.07 SIDE CHAIN REMARK 500 1 G A 8 0.06 SIDE CHAIN REMARK 500 1 G A 9 0.10 SIDE CHAIN REMARK 500 1 A A 10 0.09 SIDE CHAIN REMARK 500 1 G A 11 0.07 SIDE CHAIN REMARK 500 1 A A 12 0.12 SIDE CHAIN REMARK 500 1 C A 13 0.12 SIDE CHAIN REMARK 500 1 G A 17 0.09 SIDE CHAIN REMARK 500 1 A A 18 0.09 SIDE CHAIN REMARK 500 1 G A 20 0.10 SIDE CHAIN REMARK 500 1 C A 22 0.06 SIDE CHAIN REMARK 500 2 G A 1 0.08 SIDE CHAIN REMARK 500 2 G A 9 0.07 SIDE CHAIN REMARK 500 2 A A 10 0.08 SIDE CHAIN REMARK 500 2 G A 11 0.07 SIDE CHAIN REMARK 500 2 A A 12 0.10 SIDE CHAIN REMARK 500 2 C A 13 0.15 SIDE CHAIN REMARK 500 2 G A 17 0.08 SIDE CHAIN REMARK 500 2 A A 19 0.09 SIDE CHAIN REMARK 500 2 G A 20 0.10 SIDE CHAIN REMARK 500 3 C A 3 0.08 SIDE CHAIN REMARK 500 3 A A 7 0.08 SIDE CHAIN REMARK 500 3 G A 8 0.09 SIDE CHAIN REMARK 500 3 G A 9 0.08 SIDE CHAIN REMARK 500 3 A A 10 0.07 SIDE CHAIN REMARK 500 3 A A 12 0.12 SIDE CHAIN REMARK 500 3 C A 13 0.19 SIDE CHAIN REMARK 500 3 G A 17 0.09 SIDE CHAIN REMARK 500 3 A A 18 0.11 SIDE CHAIN REMARK 500 3 G A 20 0.12 SIDE CHAIN REMARK 500 3 C A 22 0.07 SIDE CHAIN REMARK 500 4 G A 1 0.07 SIDE CHAIN REMARK 500 4 G A 9 0.09 SIDE CHAIN REMARK 500 4 A A 10 0.09 SIDE CHAIN REMARK 500 4 G A 11 0.09 SIDE CHAIN REMARK 500 4 A A 12 0.09 SIDE CHAIN REMARK 500 4 C A 13 0.13 SIDE CHAIN REMARK 500 4 A A 16 0.07 SIDE CHAIN REMARK 500 4 A A 18 0.13 SIDE CHAIN REMARK 500 4 G A 20 0.15 SIDE CHAIN REMARK 500 5 G A 1 0.08 SIDE CHAIN REMARK 500 5 G A 6 0.08 SIDE CHAIN REMARK 500 5 A A 7 0.08 SIDE CHAIN REMARK 500 5 A A 10 0.07 SIDE CHAIN REMARK 500 5 A A 12 0.07 SIDE CHAIN REMARK 500 5 C A 13 0.14 SIDE CHAIN REMARK 500 5 U A 14 0.10 SIDE CHAIN REMARK 500 5 A A 18 0.14 SIDE CHAIN REMARK 500 5 A A 19 0.11 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 91 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1JUR A 1 22 PDB 1JUR 1JUR 1 22 SEQRES 1 A 22 G G C C U G A G G A G A C SEQRES 2 A 22 U C A G A A G C C CRYST1 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