HEADER RNA 06-SEP-02 1MNX TITLE THE SOLUTION STRUCTURE OF THE LOOP E REGION OF THE 5S RRNA FROM TITLE 2 SPINACH CHLOROPLASTS. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOOP E FROM 5S RRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 4 ORGANISM_COMMON: SPINACH; SOURCE 5 ORGANISM_TAXID: 3562; SOURCE 6 OTHER_DETAILS: RNA WAS IN VITRO TRANSCRIBED USING T7 RNA POLYMERASE SOURCE 7 FROM A LINEARIZED PLASMID CONTAINING THE REQUIRED SEQUENCE. THE SOURCE 8 SEQUENCE IS NATURALLY FOUND IN SPINACIA OLERACEA (SPINACH) SOURCE 9 CHOLORPLASTS. KEYWDS LOOP E, 5S RRNA, RNA EXPDTA SOLUTION NMR NUMMDL 13 MDLTYP MINIMIZED AVERAGE AUTHOR P.VALLURUPALLI,P.B.MOORE REVDAT 4 01-MAY-24 1MNX 1 REMARK REVDAT 3 25-MAY-16 1MNX 1 SOURCE VERSN REVDAT 2 24-FEB-09 1MNX 1 VERSN REVDAT 1 14-JAN-03 1MNX 0 JRNL AUTH P.VALLURUPALLI,P.B.MOORE JRNL TITL THE SOLUTION STRUCTURE OF THE LOOP E REGION OF THE 5S RRNA JRNL TITL 2 FROM SPINACH CHLOROPLASTS JRNL REF J.MOL.BIOL. V. 325 843 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12527295 JRNL DOI 10.1016/S0022-2836(02)01270-6 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.B.LEONTIS,E.WESTHOF REMARK 1 TITL THE 5S RRNA LOOP E: CHEMICAL PROBING AND PHYLOGENETIC DATA REMARK 1 TITL 2 VERSUS CRYSTAL STRUCTURE REMARK 1 REF RNA V. 4 1134 1998 REMARK 1 REFN ISSN 1355-8382 REMARK 1 DOI 10.1017/S1355838298980566 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.DALLAS,P.B.MOORE REMARK 1 TITL THE LOOP E-LOOP D REGION OF ESCHERICHIA COLI 5S RRNA: THE REMARK 1 TITL 2 SOLUTION STRUCTURE REVEALS AN UNUSUAL LOOP THAT MAY BE REMARK 1 TITL 3 IMPORTANT FOR BINDING RIBOSOMAL PROTEINS. REMARK 1 REF STRUCTURE V. 5 1639 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(97)00311-0 REMARK 1 REFERENCE 3 REMARK 1 AUTH C.CORRELL,B.FREEBORN,P.B.MOORE,T.A.STEITZ REMARK 1 TITL METALS, MOTIFS, AND RECOGNITION IN THE CRYSTAL STRUCTURE OF REMARK 1 TITL 2 A 5S RRNA DOMAIN REMARK 1 REF CELL(CAMBRIDGE,MASS.) V. 91 705 1997 REMARK 1 REFN ISSN 0092-8674 REMARK 1 REFERENCE 4 REMARK 1 AUTH M.LU,T.A.STEITZ REMARK 1 TITL STRUCTURE OF ESCHERICHIA COLI RIBOSOMAL PROTEIN L25 REMARK 1 TITL 2 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8-A RESOLUTION REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 2023 2000 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.97.5.2023 REMARK 1 REFERENCE 5 REMARK 1 AUTH M.STOLDT,J.WOHNERT,O.OHLENSCHLAGER,M.GORLACH,L.R.BROWN REMARK 1 TITL THE NMR STRUCTURE OF THE 5S RRNA E-DOMAIN-PROTEIN L25 REMARK 1 TITL 2 COMPLEX SHOWS PREFORMED AND INDUCED RECOGNITION REMARK 1 REF EMBO J. V. 18 6508 1999 REMARK 1 REFN ISSN 0261-4189 REMARK 1 DOI 10.1093/EMBOJ/18.22.6508 REMARK 1 REFERENCE 6 REMARK 1 AUTH P.ROMBY,E.WESTHOF,R.TOUKIFIMPA,R.MACHE,J.P.EBEL,C.EHRESMANN, REMARK 1 AUTH 2 B.EHRESMANN REMARK 1 TITL HIGHER ORDER STRUCTURE OF CHLOROPLASTIC 5S RIBOSOMAL RNA REMARK 1 TITL 2 FROM SPINACH. REMARK 1 REF BIOCHEMISTRY V. 27 4721 1988 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : FELIX 95, CNS 1.0 REMARK 3 AUTHORS : MSI (FELIX), BRUNGER, ADAMS, CLORE, DELANO, GROS, REMARK 3 GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, REMARK 3 READ, RICE, SIMONSON, WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE, DIHEDRAL, PLANARITY REMARK 3 RESTRAINTS WERE USED IN THE REMARK 3 FIRST ROUND, FOLLOWED BY DIPOLAR REMARK 3 COUPLINGS IN THE SECOND ROUND REMARK 3 (SEE PAPER FOR DETAILS) REMARK 4 REMARK 4 1MNX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-02. REMARK 100 THE DEPOSITION ID IS D_1000017041. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 50MM; 50MM REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : RNA MOLECULE (1MM-2MM) IN 50 MM REMARK 210 NACL, 2.5MM CACODYLATE, 0.1MM REMARK 210 EDTA, PH 6.0 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : (NOESY, HSQC FOR IMINO/AMINO REMARK 210 ASSIGNMENTS); (NOESY, DQF-COSY, REMARK 210 HSQC, NOESY-HMQC, HCCH COSY, REMARK 210 ETC. SEE PAPER FOR MORE DETAILS.) REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 65 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 13 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 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 DATA OBTAINED FROM REMARK 210 HOMONUCLEAR AND HETERONUCLEAR EXPERIMENTS. 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 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 U A 71 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.6 DEGREES REMARK 500 1 C A 74 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 G A 96 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 2 G A 72 C2' - C3' - O3' ANGL. DEV. = 14.5 DEGREES REMARK 500 2 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 2 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.9 DEGREES REMARK 500 2 G A 96 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 3 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.3 DEGREES REMARK 500 3 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 3 C A 74 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 G A 96 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES REMARK 500 4 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.2 DEGREES REMARK 500 4 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.0 DEGREES REMARK 500 4 C A 74 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 G A 96 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 5 U A 71 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 5 G A 72 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 5 C A 74 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 5 G A 96 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 G A 72 C2' - C3' - O3' ANGL. DEV. = 14.8 DEGREES REMARK 500 6 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.7 DEGREES REMARK 500 6 G A 72 O4' - C1' - N9 ANGL. DEV. = -6.8 DEGREES REMARK 500 6 G A 96 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 7 U A 71 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 7 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.7 DEGREES REMARK 500 7 C A 74 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 G A 96 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 8 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 8 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.4 DEGREES REMARK 500 8 C A 79 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 G A 96 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 9 U A 71 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 9 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 9 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.3 DEGREES REMARK 500 9 C A 74 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 G A 96 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 10 U A 71 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.6 DEGREES REMARK 500 10 G A 72 O4' - C1' - N9 ANGL. DEV. = -5.1 DEGREES REMARK 500 10 C A 74 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 10 U A 77 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 10 U A 80 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 10 G A 96 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 11 G A 72 C4' - C3' - C2' ANGL. DEV. = 6.5 DEGREES REMARK 500 11 G A 72 O4' - C1' - N9 ANGL. DEV. = -4.9 DEGREES REMARK 500 11 C A 74 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 59 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 G A 70 0.06 SIDE CHAIN REMARK 500 1 C A 79 0.07 SIDE CHAIN REMARK 500 1 G A 81 0.06 SIDE CHAIN REMARK 500 1 G A 85 0.07 SIDE CHAIN REMARK 500 1 G A 87 0.09 SIDE CHAIN REMARK 500 1 A A 88A 0.07 SIDE CHAIN REMARK 500 1 G A 96 0.10 SIDE CHAIN REMARK 500 2 U A 71 0.07 SIDE CHAIN REMARK 500 2 A A 73 0.05 SIDE CHAIN REMARK 500 2 C A 79 0.08 SIDE CHAIN REMARK 500 2 G A 85 0.09 SIDE CHAIN REMARK 500 2 G A 87 0.11 SIDE CHAIN REMARK 500 2 A A 88A 0.06 SIDE CHAIN REMARK 500 2 G A 88B 0.07 SIDE CHAIN REMARK 500 2 C A 91 0.08 SIDE CHAIN REMARK 500 2 C A 92 0.07 SIDE CHAIN REMARK 500 2 G A 94 0.05 SIDE CHAIN REMARK 500 2 G A 96 0.10 SIDE CHAIN REMARK 500 2 A A 104 0.06 SIDE CHAIN REMARK 500 2 C A 107 0.07 SIDE CHAIN REMARK 500 2 C A 108 0.08 SIDE CHAIN REMARK 500 3 G A 70 0.08 SIDE CHAIN REMARK 500 3 U A 71 0.09 SIDE CHAIN REMARK 500 3 G A 72 0.07 SIDE CHAIN REMARK 500 3 U A 82 0.07 SIDE CHAIN REMARK 500 3 A A 83 0.09 SIDE CHAIN REMARK 500 3 G A 85 0.06 SIDE CHAIN REMARK 500 3 G A 87 0.10 SIDE CHAIN REMARK 500 3 A A 88A 0.06 SIDE CHAIN REMARK 500 3 G A 88B 0.07 SIDE CHAIN REMARK 500 3 A A 89 0.06 SIDE CHAIN REMARK 500 3 G A 94 0.06 SIDE CHAIN REMARK 500 3 G A 96 0.14 SIDE CHAIN REMARK 500 3 C A 108 0.09 SIDE CHAIN REMARK 500 4 G A 72 0.06 SIDE CHAIN REMARK 500 4 C A 79 0.08 SIDE CHAIN REMARK 500 4 G A 85 0.07 SIDE CHAIN REMARK 500 4 C A 86 0.06 SIDE CHAIN REMARK 500 4 G A 87 0.11 SIDE CHAIN REMARK 500 4 A A 88A 0.06 SIDE CHAIN REMARK 500 4 G A 88B 0.07 SIDE CHAIN REMARK 500 4 G A 96 0.09 SIDE CHAIN REMARK 500 5 C A 79 0.10 SIDE CHAIN REMARK 500 5 G A 85 0.08 SIDE CHAIN REMARK 500 5 G A 87 0.15 SIDE CHAIN REMARK 500 5 A A 89 0.07 SIDE CHAIN REMARK 500 5 G A 96 0.10 SIDE CHAIN REMARK 500 5 A A 104 0.06 SIDE CHAIN REMARK 500 6 G A 70 0.08 SIDE CHAIN REMARK 500 6 G A 85 0.10 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 137 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1MNX A 68 108 PDB 1MNX 1MNX 68 108 SEQRES 1 A 42 G G G U G A C G A U A C U SEQRES 2 A 42 G U A G G C G A G A G C C SEQRES 3 A 42 U G C G G A A A A A U A G SEQRES 4 A 42 C C 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 MODEL 1