Header list of 1osw.pdb file
Complete list - b 23 2 Bytes
HEADER RNA 20-MAR-03 1OSW
TITLE THE STEM OF SL1 RNA IN HIV-1: STRUCTURE AND NUCLEOCAPSID PROTEIN
TITLE 2 BINDING FOR A 1X3 INTERNAL LOOP
CAVEAT 1OSW CHIRALITY ERRORS EXIST IN SOME MODELS.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*AP*GP*GP*CP*GP*CP*UP*AP*CP*GP*GP*CP*GP*AP*GP*GP
COMPND 3 *CP*UP*CP*CP*A)-3';
COMPND 4 CHAIN: A;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: STEM OF SL1 RNA
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: RNA SEQUENCE OBTAINED FROM DHARMACON
KEYWDS RNA
EXPDTA SOLUTION NMR
NUMMDL 23
AUTHOR Y.YUAN,D.J.KERWOOD,A.C.PAOLETTI,M.F.SHUBSDA,P.N.BORER
REVDAT 3 23-FEB-22 1OSW 1 REMARK
REVDAT 2 24-FEB-09 1OSW 1 VERSN
REVDAT 1 20-MAY-03 1OSW 0
JRNL AUTH Y.YUAN,D.J.KERWOOD,A.C.PAOLETTI,M.F.SHUBSDA,P.N.BORER
JRNL TITL STEM OF SL1 RNA IN HIV-1: STRUCTURE AND NUCLEOCAPSID PROTEIN
JRNL TITL 2 BINDING FOR A 1X3 INTERNAL LOOP
JRNL REF BIOCHEMISTRY V. 42 5259 2003
JRNL REFN ISSN 0006-2960
JRNL PMID 12731867
JRNL DOI 10.1021/BI034084A
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, AMBER 5.0
REMARK 3 AUTHORS : BRUKER (XWINNMR), UNIVERSITY OF CALIFORNIA, SAN
REMARK 3 FRANCISCO (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1OSW COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-03.
REMARK 100 THE DEPOSITION ID IS D_1000018635.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 300; 278
REMARK 210 PH : 6.3; 5.5
REMARK 210 IONIC STRENGTH : 25 MM NACL; 25 MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1 MM SL1I RNA; 25MM NACL, 5MM
REMARK 210 SODIUM PHOSPHATE, 0.1MM EDTA,
REMARK 210 0.01% NAN3
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; HP-COSY; H-C
REMARK 210 HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRZ/TRIAD 6.1, MARDIGRAS 3.2,
REMARK 210 DYANA 1.5
REMARK 210 METHOD USED : DYANA FOLLOWED BY MOLECULAR
REMARK 210 DYNAMICS USING AMBER
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH THE LEAST RESTRAINT
REMARK 210 VIOLATIONS,STRUCTURES WITH THE
REMARK 210 LOWEST ENERGY,TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 17
REMARK 210
REMARK 210 REMARK: STRUCTURES WERE DETERMINED USING 2D NOESY AT DIFFERENT
REMARK 210 TEMPERATURES AND MIXING TIMES. THE LAST RESIDUE, A23, WAS
REMARK 210 ELIMINATED FROM THE PDB FILE DUE TO AMBIGUITY IN ORIENTATION.
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 MODELS 1-23
REMARK 465 RES C SSSEQI
REMARK 465 A A 23
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 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 C A 14 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 G A 18 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES
REMARK 500 1 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 3 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 4 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 4 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 4 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 5 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 6 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 6 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 7 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 7 G A 12 C1' - O4' - C4' ANGL. DEV. = -4.3 DEGREES
REMARK 500 7 C A 14 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 7 C A 21 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 8 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 8 C A 21 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 8 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 9 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 9 C A 19 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES
REMARK 500 10 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 10 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 10 G A 17 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES
REMARK 500 11 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 11 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 12 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 13 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 13 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 14 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 15 G A 18 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 15 G A 18 C3' - O3' - P ANGL. DEV. = 8.3 DEGREES
REMARK 500 16 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 16 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 16 C A 19 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 16 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 17 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 17 G A 12 N3 - C4 - C5 ANGL. DEV. = -3.1 DEGREES
REMARK 500 18 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 18 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 18 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 19 C A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 19 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 19 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 20 G A 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES
REMARK 500 20 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 20 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 20 U A 20 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 61 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 12 0.07 SIDE CHAIN
REMARK 500 2 G A 7 0.06 SIDE CHAIN
REMARK 500 2 C A 14 0.07 SIDE CHAIN
REMARK 500 3 G A 4 0.07 SIDE CHAIN
REMARK 500 3 G A 18 0.07 SIDE CHAIN
REMARK 500 4 U A 9 0.07 SIDE CHAIN
REMARK 500 4 G A 18 0.08 SIDE CHAIN
REMARK 500 4 U A 20 0.06 SIDE CHAIN
REMARK 500 4 C A 21 0.07 SIDE CHAIN
REMARK 500 5 C A 6 0.08 SIDE CHAIN
REMARK 500 5 G A 18 0.06 SIDE CHAIN
REMARK 500 6 G A 12 0.06 SIDE CHAIN
REMARK 500 6 G A 13 0.08 SIDE CHAIN
REMARK 500 7 G A 7 0.06 SIDE CHAIN
REMARK 500 7 U A 9 0.07 SIDE CHAIN
REMARK 500 7 G A 12 0.06 SIDE CHAIN
REMARK 500 7 C A 19 0.10 SIDE CHAIN
REMARK 500 7 U A 20 0.07 SIDE CHAIN
REMARK 500 8 U A 9 0.10 SIDE CHAIN
REMARK 500 8 C A 21 0.06 SIDE CHAIN
REMARK 500 9 U A 9 0.08 SIDE CHAIN
REMARK 500 9 G A 18 0.09 SIDE CHAIN
REMARK 500 10 U A 9 0.07 SIDE CHAIN
REMARK 500 11 G A 1 0.06 SIDE CHAIN
REMARK 500 11 G A 18 0.08 SIDE CHAIN
REMARK 500 13 U A 9 0.09 SIDE CHAIN
REMARK 500 13 G A 13 0.08 SIDE CHAIN
REMARK 500 13 G A 18 0.05 SIDE CHAIN
REMARK 500 13 U A 20 0.06 SIDE CHAIN
REMARK 500 14 G A 4 0.06 SIDE CHAIN
REMARK 500 14 U A 9 0.08 SIDE CHAIN
REMARK 500 14 G A 12 0.06 SIDE CHAIN
REMARK 500 14 G A 18 0.05 SIDE CHAIN
REMARK 500 15 G A 7 0.05 SIDE CHAIN
REMARK 500 15 G A 12 0.05 SIDE CHAIN
REMARK 500 16 C A 11 0.09 SIDE CHAIN
REMARK 500 17 G A 7 0.06 SIDE CHAIN
REMARK 500 17 C A 19 0.08 SIDE CHAIN
REMARK 500 17 C A 21 0.08 SIDE CHAIN
REMARK 500 18 C A 11 0.07 SIDE CHAIN
REMARK 500 18 C A 14 0.07 SIDE CHAIN
REMARK 500 19 G A 17 0.06 SIDE CHAIN
REMARK 500 19 G A 18 0.06 SIDE CHAIN
REMARK 500 20 G A 7 0.06 SIDE CHAIN
REMARK 500 20 C A 19 0.09 SIDE CHAIN
REMARK 500 21 G A 7 0.06 SIDE CHAIN
REMARK 500 21 G A 12 0.06 SIDE CHAIN
REMARK 500 21 A A 16 0.06 SIDE CHAIN
REMARK 500 22 G A 5 0.05 SIDE CHAIN
REMARK 500 22 G A 7 0.06 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 57 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1OSW A 1 23 PDB 1OSW 1OSW 1 23
SEQRES 1 A 23 G G A G G C G C U A C G G
SEQRES 2 A 23 C G A G G C U C C A
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 - b 23 2 Bytes