Header list of 1r7z.pdb file
Complete list - r 2 2 Bytes
HEADER RNA 22-OCT-03 1R7Z
TITLE NMR STRUCTURE OF THE R(GGAGGACAUUCCUCACGGGUGACCGUGGUCCUCC), DOMAIN IV
TITLE 2 STEM-LOOP B OF ENTEROVIRAL IRES WITH AUUCCU BULGE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 34-MER;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: DOMAIN IV, LOOP B;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: RNA FRAGMENT OF ENTEROVIRAL IRES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7
SOURCE 4 RNA POLYMERASE
KEYWDS STEM-AND-LOOP STRUCTURE, SIX-NUCLEOTIDE BULGE, GUGA TETRALOOP, RNA
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR Z.DU,N.B.ULYANOV,J.YU,T.L.JAMES
REVDAT 3 02-MAR-22 1R7Z 1 REMARK
REVDAT 2 24-FEB-09 1R7Z 1 VERSN
REVDAT 1 25-MAY-04 1R7Z 0
JRNL AUTH Z.DU,N.B.ULYANOV,J.YU,R.ANDINO,T.L.JAMES
JRNL TITL NMR STRUCTURES OF LOOP B RNAS FROM THE STEM-LOOP IV DOMAIN
JRNL TITL 2 OF THE ENTEROVIRUS INTERNAL RIBOSOME ENTRY SITE: A SINGLE C
JRNL TITL 3 TO U SUBSTITUTION DRASTICALLY CHANGES THE SHAPE AND
JRNL TITL 4 FLEXIBILITY OF RNA(,).
JRNL REF BIOCHEMISTRY V. 43 5757 2004
JRNL REFN ISSN 0006-2960
JRNL PMID 15134450
JRNL DOI 10.1021/BI0363228
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 6.1, DYANA 1.5, AMBER 7
REMARK 3 AUTHORS : VARIAN ASSOCIATES, INC. (VNMR), P.GUNTERT (DYANA),
REMARK 3 D.A.CASE (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE REFINED BASED ON 614 NOE
REMARK 3 -DERIVED DISTANCES AND 26 RESIDUAL DIPOLAR COUPLINGS
REMARK 4
REMARK 4 1R7Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-03.
REMARK 100 THE DEPOSITION ID IS D_1000020549.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 298
REMARK 210 PH : 6.5; 6.5
REMARK 210 IONIC STRENGTH : 50 MM NA+ IONS; 50 MM NA+ IONS
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1MM UNLABELED RNA, 25MM NACL,
REMARK 210 25MM SODIUM PHOSPHATE BUFFER (PH
REMARK 210 6.5), 90% H2O; 10% D2O; 1MM
REMARK 210 UNLABELED RNA, 25MM NACL, 25MM
REMARK 210 SODIUM PHOSPHATE BUFFER (PH 6.5),
REMARK 210 D2O; 1MM OF RNA LABELED IN
REMARK 210 RESIDUES A AND U WITH 13C, 15N,
REMARK 210 25MM NACL, 25MM SODIUM PHOSPHATE
REMARK 210 BUFFER (PH 6.5), 5% (WEIGHT/
REMARK 210 VOLUME) OF C12E6/N-HEXANOL
REMARK 210 MIXTURE (MOLAR RATIO 0.64), D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 1H-13C
REMARK 210 CONSTANT TIME HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 2.1, MARDIGRAS 3.2
REMARK 210 METHOD USED : FULL MATRIX RELAXATION ANALYSIS
REMARK 210 OF NOE, RANDOM ERROR ANALYSIS OF
REMARK 210 NOE, SIMULATED ANNEALING USING
REMARK 210 RESTRAINED MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TOTAL ENERGY (A WEIGHTED
REMARK 210 SUM OF CONFORMATIONAL ENERGY AND
REMARK 210 RESTRAINT ENERGY)
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: 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 13 U A 13 P U A 13 O5' 0.060
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1R7W RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF THE R(GGAGGACAUCCCUCACGGGUGACCGUGGUCCUCC), DOMAIN
REMARK 900 IV STEM-LOOP B OF ENTEROVIRAL IRES WITH AUCCCU BULGE
DBREF 1R7Z A 1 34 PDB 1R7Z 1R7Z 1 34
SEQRES 1 A 34 G G A G G A C A U U C C U
SEQRES 2 A 34 C A C G G G U G A C C G U
SEQRES 3 A 34 G G U C C U 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
Complete list - r 2 2 Bytes