Header list of 2d19.pdb file
Complete list - r 9 2 Bytes
HEADER RNA 15-AUG-05 2D19
TITLE SOLUTION RNA STRUCTURE OF LOOP REGION OF THE HIV-1 DIMERIZATION
TITLE 2 INITIATION SITE IN THE KISSING-LOOP DIMER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-
COMPND 3 3';
COMPND 4 CHAIN: A, B;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS DIS, HIV-1, RNA
EXPDTA SOLUTION NMR
NUMMDL 11
MDLTYP MINIMIZED AVERAGE
AUTHOR S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI,N.YAMAMOTO,G.KAWAI
REVDAT 3 09-MAR-22 2D19 1 REMARK
REVDAT 2 24-FEB-09 2D19 1 VERSN
REVDAT 1 01-NOV-05 2D19 0
JRNL AUTH S.BABA,K.TAKAHASHI,S.NOGUCHI,H.TAKAKU,Y.KOYANAGI,N.YAMAMOTO,
JRNL AUTH 2 G.KAWAI
JRNL TITL SOLUTION RNA STRUCTURES OF THE HIV-1 DIMERIZATION INITIATION
JRNL TITL 2 SITE IN THE KISSING-LOOP AND EXTENDED-DUPLEX DIMERS.
JRNL REF J.BIOCHEM.(TOKYO) V. 138 583 2005
JRNL REFN ISSN 0021-924X
JRNL PMID 16272570
JRNL DOI 10.1093/JB/MVI158
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XWINNMR 2.6, DISCOVER 97.0
REMARK 3 AUTHORS : BRUKER (XWINNMR), ACCELRYS (DISCOVER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF
REMARK 3 502 RESTRAINTS, 286 ARE NOE-DERIVED DISTANCE CONSTRAINTS, 140
REMARK 3 DIHEDRAL ANGLE RESTRAINTS, 76 DISTANCE RESTRAINTS FROM HYDROGEN
REMARK 3 BONDS.
REMARK 4
REMARK 4 2D19 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-AUG-05.
REMARK 100 THE DEPOSITION ID IS D_1000024862.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 283; 298
REMARK 210 PH : 7.0; 7.0
REMARK 210 IONIC STRENGTH : 50MM NACL; 50MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.8MM 25-MER RNA FRAGMENT; 10MM
REMARK 210 PHOSPHATE BUFFER, 50MM NACL; 100%
REMARK 210 D2O; 1.8MM 25-MER RNA FRAGMENT;
REMARK 210 10MM PHOSPHATE BUFFER, 50MM NACL;
REMARK 210 90% H2O, 10% D2O; 0.3MM [G-13C/
REMARK 210 15N] LABELED 39-MER RNA FRAGMENT;
REMARK 210 10MM PHOSPHATE BUFFER, 50MM
REMARK 210 NACL; 100% D2O; 0.3MM [G-13C/15N]
REMARK 210 LABELED 39-MER RNA FRAGMENT;
REMARK 210 10MM PHOSPHATE BUFFER, 50MM NACL;
REMARK 210 90% H2O, 10% D2O; 0.1MM [A-13C/
REMARK 210 15N] LABELED 39-MER RNA FRAGMENT;
REMARK 210 10MM PHOSPHATE BUFFER, 50MM
REMARK 210 NACL; 100% D2O; 1.0MM 39-MER RNA
REMARK 210 FRAGMENT; 10MM PHOSPHATE BUFFER,
REMARK 210 50MM NACL; 100% D2O; 1.0MM 39-
REMARK 210 MER RNA FRAGMENT; 10MM PHOSPHATE
REMARK 210 BUFFER, 50MM NACL; 90% H2O, 10%
REMARK 210 D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 1D-HSQC-SELECTED
REMARK 210 SPECTRUM; 1D-HSQC-FILTERED
REMARK 210 SPECTRUM; 2D TOCSY; 2D-W2-
REMARK 210 FILTERED NOESY
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 : FELIX 97.0, DISCOVER 97.0
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK:
REMARK 210 CHEMICAL SYNTHESIZED 25-MER RNA CORRESPONDING TO THE HIV-1
REMARK 210 DIMERIZATION INITIATION SITE.
REMARK 210 ENZYMATICAL SYNTHESIZED [G-13C/15N] LABELED 39-MER RNA
REMARK 210 CORRESPONDING TO THE HIV-1 DIMERIZATION INITIATION SITE.
REMARK 210 ENZYMATICAL SYNTHESIZED [A-13C/15N] LABELED 39-MER RNA
REMARK 210 CORRESPONDING TO THE HIV-1 DIMERIZATION INITIATION SITE.
REMARK 210 ENZYMATICAL SYNTHESIZED 39-MER RNA CORRESPONDING TO THE HIV-1
REMARK 210 DIMERIZATION INITIATION SITE.
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 C A 2 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 1 A A 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 1 C A 10 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES
REMARK 500 1 A A 11 O4' - C1' - N9 ANGL. DEV. = 9.1 DEGREES
REMARK 500 1 C A 12 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 C A 14 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 C B 2 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 U B 3 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 1 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 1 C B 10 O4' - C1' - N1 ANGL. DEV. = 6.4 DEGREES
REMARK 500 1 A B 11 O4' - C1' - N9 ANGL. DEV. = 8.2 DEGREES
REMARK 500 1 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 C B 14 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 1 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 2 C A 2 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 2 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 2 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 2 C A 10 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 2 A A 11 O4' - C1' - N9 ANGL. DEV. = 8.1 DEGREES
REMARK 500 2 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 2 A A 13 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 C A 14 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 C B 2 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 2 U B 3 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 2 G B 7 O4' - C1' - N9 ANGL. DEV. = 7.1 DEGREES
REMARK 500 2 U B 8 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 C B 10 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES
REMARK 500 2 A B 11 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES
REMARK 500 2 C B 12 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 2 A B 13 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES
REMARK 500 2 C B 14 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 C B 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 C A 2 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 3 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.8 DEGREES
REMARK 500 3 G A 7 O4' - C1' - N9 ANGL. DEV. = 7.3 DEGREES
REMARK 500 3 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 3 C A 10 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 3 A A 11 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES
REMARK 500 3 C A 12 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 3 C A 14 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 3 C A 17 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 C B 2 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 3 U B 3 O4' - C1' - N1 ANGL. DEV. = 6.7 DEGREES
REMARK 500 3 U B 8 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 3 C B 10 O4' - C1' - N1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 3 A B 11 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 187 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 A A 6 0.07 SIDE CHAIN
REMARK 500 1 A A 11 0.07 SIDE CHAIN
REMARK 500 1 U B 3 0.06 SIDE CHAIN
REMARK 500 1 A B 5 0.06 SIDE CHAIN
REMARK 500 1 G B 9 0.07 SIDE CHAIN
REMARK 500 1 A B 11 0.07 SIDE CHAIN
REMARK 500 2 A A 5 0.06 SIDE CHAIN
REMARK 500 2 G A 7 0.07 SIDE CHAIN
REMARK 500 2 U B 8 0.07 SIDE CHAIN
REMARK 500 3 U A 8 0.06 SIDE CHAIN
REMARK 500 3 C A 14 0.07 SIDE CHAIN
REMARK 500 3 A B 5 0.10 SIDE CHAIN
REMARK 500 3 G B 9 0.07 SIDE CHAIN
REMARK 500 4 G A 4 0.06 SIDE CHAIN
REMARK 500 4 G A 9 0.06 SIDE CHAIN
REMARK 500 4 G B 1 0.05 SIDE CHAIN
REMARK 500 4 U B 3 0.07 SIDE CHAIN
REMARK 500 4 A B 5 0.09 SIDE CHAIN
REMARK 500 4 A B 11 0.07 SIDE CHAIN
REMARK 500 4 C B 14 0.09 SIDE CHAIN
REMARK 500 5 U B 3 0.06 SIDE CHAIN
REMARK 500 5 G B 7 0.10 SIDE CHAIN
REMARK 500 5 C B 14 0.07 SIDE CHAIN
REMARK 500 6 A A 5 0.10 SIDE CHAIN
REMARK 500 6 U A 8 0.06 SIDE CHAIN
REMARK 500 6 C A 14 0.08 SIDE CHAIN
REMARK 500 6 G B 1 0.05 SIDE CHAIN
REMARK 500 6 A B 5 0.08 SIDE CHAIN
REMARK 500 7 G A 7 0.07 SIDE CHAIN
REMARK 500 7 C A 10 0.06 SIDE CHAIN
REMARK 500 7 A A 11 0.07 SIDE CHAIN
REMARK 500 7 G B 9 0.06 SIDE CHAIN
REMARK 500 8 A A 11 0.08 SIDE CHAIN
REMARK 500 8 C A 14 0.06 SIDE CHAIN
REMARK 500 8 G B 1 0.05 SIDE CHAIN
REMARK 500 8 U B 3 0.08 SIDE CHAIN
REMARK 500 8 A B 5 0.07 SIDE CHAIN
REMARK 500 8 G B 9 0.06 SIDE CHAIN
REMARK 500 8 C B 14 0.07 SIDE CHAIN
REMARK 500 9 C A 10 0.06 SIDE CHAIN
REMARK 500 9 A B 5 0.10 SIDE CHAIN
REMARK 500 9 G B 9 0.05 SIDE CHAIN
REMARK 500 9 A B 11 0.07 SIDE CHAIN
REMARK 500 9 C B 14 0.07 SIDE CHAIN
REMARK 500 10 G A 1 0.06 SIDE CHAIN
REMARK 500 10 U A 3 0.07 SIDE CHAIN
REMARK 500 10 A A 5 0.06 SIDE CHAIN
REMARK 500 10 A A 11 0.07 SIDE CHAIN
REMARK 500 10 C A 14 0.07 SIDE CHAIN
REMARK 500 10 U B 3 0.06 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2D17 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF STEM-BULGE-STEM REGION OF DIS
REMARK 900 RELATED ID: 2D18 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF LOOP REGION OF THE EXTENDED-DUPLEX DIMER
REMARK 900 RELATED ID: 2D1A RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE MODEL OF THE EXTENDED-DUPLEX DIMER
REMARK 900 RELATED ID: 2D1B RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE MODELS OF THE KISSING-LOOP DIMER
DBREF 2D19 A 1 17 PDB 2D19 2D19 1 17
DBREF 2D19 B 1 17 PDB 2D19 2D19 1 17
SEQRES 1 A 17 G C U G A A G U G C A C A
SEQRES 2 A 17 C G G C
SEQRES 1 B 17 G C U G A A G U G C A C A
SEQRES 2 B 17 C G G 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 9 2 Bytes