Header list of 1fqz.pdb file
Complete list - 23 202 Bytes
HEADER RNA 07-SEP-00 1FQZ
TITLE NMR VALIDATED MODEL OF DOMAIN IIID OF HEPATITIS C VIRUS INTERNAL
TITLE 2 RIBOSOME ENTRY SITE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HEPATITIS C VIRUS IRES DOMAIN IIID;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: TRANSCRIBED USING T7 RNA POLYMERASE
KEYWDS TRANS WOBBLE G.U PAIR, S-TURN, SARCIN-RICIN LOOP, LOOP E MOTIF,
KEYWDS 2 SHEARED G.A PAIR, REVERSE HOOGSTEEN A.U PAIR, RNA
EXPDTA SOLUTION NMR
AUTHOR R.KLINCK,E.WESTHOF,S.WALKER,M.AFSHAR,A.COLLIER,F.ABOUL-ELA
REVDAT 4 23-FEB-22 1FQZ 1 REMARK
REVDAT 3 24-FEB-09 1FQZ 1 VERSN
REVDAT 2 01-APR-03 1FQZ 1 JRNL
REVDAT 1 17-JAN-01 1FQZ 0
JRNL AUTH R.KLINCK,E.WESTHOF,S.WALKER,M.AFSHAR,A.COLLIER,F.ABOUL-ELA
JRNL TITL A POTENTIAL RNA DRUG TARGET IN THE HEPATITIS C VIRUS
JRNL TITL 2 INTERNAL RIBOSOMAL ENTRY SITE.
JRNL REF RNA V. 6 1423 2000
JRNL REFN ISSN 1355-8382
JRNL PMID 11073218
JRNL DOI 10.1017/S1355838200000935
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.5, CHARMM 25.2, INSIGHT II 97.0
REMARK 3 AUTHORS : BRUKER (XWINNMR), BROOKS ET AL. (CHARMM), MSI
REMARK 3 (INSIGHT II)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: MOTIFS (I) TO (VI) WERE OBTAINED FROM
REMARK 3 THE FOLLOWING SOURCES: (I) IDEALIZED A-FORM COORDINATES
REMARK 3 (INSIGHTII, MSI); (II)&(III) PDB 430D.PDB; (IV) PDB 1ETG.PDB;
REMARK 3 (VI) PDB 1QA6.PDB; MOTIF (V) WAS CONSTRUCTED MANUALLY.
REMARK 4
REMARK 4 1FQZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-00.
REMARK 100 THE DEPOSITION ID IS D_1000011837.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 278; 298; 303
REMARK 210 PH : 6.6; 6.6; 6.6
REMARK 210 IONIC STRENGTH : 8MM NA PHOSPHATE; 8MM NA
REMARK 210 PHOSPHATE; 8MM NA PHOSPHATE
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.2 MM RNA, 8MM SODIUM PHOSPHATE
REMARK 210 BUFFER PH 6.6; 1.2 MM RNA, 8MM
REMARK 210 SODIUM PHOSPHATE BUFFER PH 6.6
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRPIPE 1.7, SPARKY 3.66
REMARK 210 METHOD USED : USING A MOTIF-BASED APPROACH, A
REMARK 210 MODEL WAS CONSTRUCTED FROM X-RAY
REMARK 210 AND NMR STRUCTURES OF 6 KNOWN
REMARK 210 RNA MOTIFS: (I) DOUBLE HELIX,
REMARK 210 (II) SHEARED G.A BASE PAIR, (III)
REMARK 210 EUKARYOTIC LOOP E MOTIF, (IV) S-
REMARK 210 TURN, (V) TRANS WOBBLE G.U PAIR,
REMARK 210 (VI) U-TURN. THE RESULTING
REMARK 210 ENERGY MINIMIZED MODEL WAS THEN
REMARK 210 VALIDATED BY COMPARING IT WITH
REMARK 210 THE NOESY DATA.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 1
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY, STRUCTURES
REMARK 210 WITH FAVORABLE NON-BOND ENERGY
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 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 7 C2 U A 7 N3 0.042
REMARK 500 U A 10 C2 U A 10 N3 0.045
REMARK 500 U A 13 C2 U A 13 N3 0.046
REMARK 500 U A 17 C2 U A 17 N3 0.046
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 G A 1 N3 - C2 - N2 ANGL. DEV. = 6.4 DEGREES
REMARK 500 G A 1 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES
REMARK 500 C A 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 G A 4 N3 - C2 - N2 ANGL. DEV. = 6.7 DEGREES
REMARK 500 A A 5 N1 - C6 - N6 ANGL. DEV. = 6.7 DEGREES
REMARK 500 G A 6 N3 - C2 - N2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 A A 8 N1 - C6 - N6 ANGL. DEV. = 6.6 DEGREES
REMARK 500 G A 9 N3 - C2 - N2 ANGL. DEV. = 6.4 DEGREES
REMARK 500 G A 11 N3 - C2 - N2 ANGL. DEV. = 6.8 DEGREES
REMARK 500 G A 11 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G A 11 C5 - C6 - O6 ANGL. DEV. = -3.6 DEGREES
REMARK 500 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 G A 14 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES
REMARK 500 G A 15 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES
REMARK 500 G A 15 N1 - C6 - O6 ANGL. DEV. = 3.6 DEGREES
REMARK 500 G A 16 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES
REMARK 500 G A 16 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 G A 16 C5 - C6 - O6 ANGL. DEV. = -3.7 DEGREES
REMARK 500 G A 19 N3 - C2 - N2 ANGL. DEV. = 6.5 DEGREES
REMARK 500 G A 19 N1 - C6 - O6 ANGL. DEV. = 3.8 DEGREES
REMARK 500 G A 19 C5 - C6 - O6 ANGL. DEV. = -3.8 DEGREES
REMARK 500 C A 20 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 G A 21 N3 - C2 - N2 ANGL. DEV. = 7.0 DEGREES
REMARK 500 G A 21 N1 - C6 - O6 ANGL. DEV. = 3.6 DEGREES
REMARK 500 A A 22 N1 - C6 - N6 ANGL. DEV. = 6.6 DEGREES
REMARK 500 A A 23 N1 - C6 - N6 ANGL. DEV. = 6.9 DEGREES
REMARK 500 A A 24 N1 - C6 - N6 ANGL. DEV. = 6.9 DEGREES
REMARK 500 G A 25 N3 - C2 - N2 ANGL. DEV. = 6.2 DEGREES
REMARK 500 G A 25 N1 - C6 - O6 ANGL. DEV. = 3.7 DEGREES
REMARK 500 G A 26 N3 - C2 - N2 ANGL. DEV. = 6.1 DEGREES
REMARK 500 G A 26 N1 - C6 - O6 ANGL. DEV. = 3.6 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 U A 12 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1FQZ A 1 27 PDB 1FQZ 1FQZ 1 27
SEQRES 1 A 27 G C C G A G U A G U G U U
SEQRES 2 A 27 G G G U C G C G A A A G G
SEQRES 3 A 27 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
Complete list - 23 202 Bytes