Header list of 2ixy.pdb file
Complete list - y 9 2 Bytes
HEADER RNA 11-JUL-06 2IXY
TITLE SOLUTION STRUCTURE OF THE APICAL STEM-LOOP OF THE HUMAN HEPATITIS B
TITLE 2 VIRUS ENCAPSIDATION SIGNAL
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-R(*GP*GP*CP*CP*UP*CP*CP*AP*AP*GP
COMPND 3 *CP*UP*GP*UP*GP*CP*CP*UP*UP*GP*GP*GP*UP*GP*GP*CP*C)-3';
COMPND 4 CHAIN: A;
COMPND 5 SYNONYM: APICAL STEM-LOOP FROM HBV EPSILON;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HEPATITIS B VIRUS;
SOURCE 4 ORGANISM_TAXID: 10407
KEYWDS HBV, RDC, RNA, PSEUDO TRILOOP
EXPDTA SOLUTION NMR
NUMMDL 23
AUTHOR S.FLODELL,M.PETERSEN,F.GIRARD,J.ZDUNEK,K.KIDD-LJUNGGREN,J.SCHLEUCHER,
AUTHOR 2 S.S.WIJMENGA
REVDAT 4 09-MAY-18 2IXY 1 JRNL REMARK
REVDAT 3 24-FEB-09 2IXY 1 VERSN
REVDAT 2 18-OCT-06 2IXY 1 JRNL
REVDAT 1 06-SEP-06 2IXY 0
JRNL AUTH S.FLODELL,M.PETERSEN,F.GIRARD,J.ZDUNEK,K.KIDD-LJUNGGREN,
JRNL AUTH 2 J.SCHLEUCHER,S.WIJMENGA
JRNL TITL SOLUTION STRUCTURE OF THE APICAL STEM-LOOP OF THE HUMAN
JRNL TITL 2 HEPATITIS B VIRUS ENCAPSIDATION SIGNAL.
JRNL REF NUCLEIC ACIDS RES. V. 34 4449 2006
JRNL REFN ESSN 1362-4962
JRNL PMID 16945960
JRNL DOI 10.1093/NAR/GKL582
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR
REMARK 3 AUTHORS : BRUNGER
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE
REMARK 4
REMARK 4 2IXY COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-06.
REMARK 100 THE DEPOSITION ID IS D_1290029308.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298.0
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 100
REMARK 210 PRESSURE : 1.0 ATM
REMARK 210 SAMPLE CONTENTS : D2O, 10% D2O/90% H2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : DRX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 23
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: NONE
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 2 A A 8 N3 A A 8 C4 0.039
REMARK 500 5 A A 8 N3 A A 8 C4 0.037
REMARK 500 6 A A 8 N3 A A 8 C4 0.037
REMARK 500 7 A A 8 N3 A A 8 C4 0.044
REMARK 500 8 A A 8 N3 A A 8 C4 0.036
REMARK 500 9 A A 8 N3 A A 8 C4 0.036
REMARK 500 10 A A 8 N3 A A 8 C4 0.037
REMARK 500 11 A A 8 N3 A A 8 C4 0.037
REMARK 500 13 A A 8 N3 A A 8 C4 0.038
REMARK 500 14 A A 8 N3 A A 8 C4 0.038
REMARK 500 15 A A 8 N3 A A 8 C4 0.037
REMARK 500 16 A A 8 N3 A A 8 C4 0.044
REMARK 500 17 A A 8 N3 A A 8 C4 0.037
REMARK 500 22 A A 8 N3 A A 8 C4 0.036
REMARK 500 23 A A 8 N3 A A 8 C4 0.042
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 1 G A 2 N3 - C4 - C5 ANGL. DEV. = -3.0 DEGREES
REMARK 500 1 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 C A 4 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 1 U A 5 O4' - C1' - N1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 1 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 C A 7 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 A A 8 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 U A 14 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES
REMARK 500 1 U A 14 C4 - C5 - C6 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 U A 14 C5 - C6 - N1 ANGL. DEV. = -3.0 DEGREES
REMARK 500 1 G A 15 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 G A 15 N7 - C8 - N9 ANGL. DEV. = 3.3 DEGREES
REMARK 500 1 G A 15 C8 - N9 - C4 ANGL. DEV. = -3.0 DEGREES
REMARK 500 1 C A 16 O4' - C4' - C3' ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 C A 16 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES
REMARK 500 1 C A 17 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES
REMARK 500 1 U A 18 O4' - C1' - N1 ANGL. DEV. = 7.6 DEGREES
REMARK 500 1 U A 19 O4' - C1' - N1 ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 G A 21 N3 - C4 - C5 ANGL. DEV. = -3.2 DEGREES
REMARK 500 1 G A 22 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 U A 23 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 1 G A 24 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 C A 26 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 C A 27 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 C A 3 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 2 C A 4 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES
REMARK 500 2 U A 5 O4' - C1' - N1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 2 C A 6 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 C A 7 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 2 C A 7 C6 - N1 - C2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 2 C A 7 N3 - C4 - C5 ANGL. DEV. = -2.7 DEGREES
REMARK 500 2 C A 7 C5 - C6 - N1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 A A 8 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 G A 10 N3 - C4 - C5 ANGL. DEV. = -4.0 DEGREES
REMARK 500 2 G A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES
REMARK 500 2 U A 12 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 G A 13 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES
REMARK 500 2 U A 14 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 G A 15 N3 - C4 - C5 ANGL. DEV. = -3.6 DEGREES
REMARK 500 2 G A 15 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES
REMARK 500 2 G A 15 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES
REMARK 500 2 C A 16 O4' - C4' - C3' ANGL. DEV. = -8.5 DEGREES
REMARK 500 2 C A 16 C1' - O4' - C4' ANGL. DEV. = -5.2 DEGREES
REMARK 500 2 C A 16 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES
REMARK 500 2 C A 17 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES
REMARK 500 2 C A 17 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES
REMARK 500 2 U A 18 O4' - C1' - N1 ANGL. DEV. = 6.5 DEGREES
REMARK 500 2 U A 19 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES
REMARK 500 2 G A 22 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 601 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 C A 3 0.08 SIDE CHAIN
REMARK 500 1 C A 4 0.07 SIDE CHAIN
REMARK 500 1 U A 5 0.07 SIDE CHAIN
REMARK 500 1 A A 9 0.09 SIDE CHAIN
REMARK 500 1 G A 10 0.09 SIDE CHAIN
REMARK 500 1 U A 14 0.14 SIDE CHAIN
REMARK 500 1 C A 17 0.15 SIDE CHAIN
REMARK 500 1 U A 18 0.14 SIDE CHAIN
REMARK 500 2 C A 3 0.08 SIDE CHAIN
REMARK 500 2 C A 4 0.08 SIDE CHAIN
REMARK 500 2 U A 5 0.07 SIDE CHAIN
REMARK 500 2 A A 9 0.07 SIDE CHAIN
REMARK 500 2 G A 13 0.05 SIDE CHAIN
REMARK 500 2 U A 14 0.22 SIDE CHAIN
REMARK 500 2 C A 17 0.18 SIDE CHAIN
REMARK 500 2 U A 18 0.09 SIDE CHAIN
REMARK 500 2 G A 22 0.05 SIDE CHAIN
REMARK 500 3 C A 3 0.08 SIDE CHAIN
REMARK 500 3 C A 4 0.06 SIDE CHAIN
REMARK 500 3 U A 5 0.06 SIDE CHAIN
REMARK 500 3 A A 9 0.07 SIDE CHAIN
REMARK 500 3 G A 10 0.08 SIDE CHAIN
REMARK 500 3 U A 14 0.12 SIDE CHAIN
REMARK 500 3 C A 17 0.14 SIDE CHAIN
REMARK 500 3 U A 18 0.16 SIDE CHAIN
REMARK 500 3 U A 19 0.06 SIDE CHAIN
REMARK 500 4 C A 3 0.09 SIDE CHAIN
REMARK 500 4 C A 4 0.08 SIDE CHAIN
REMARK 500 4 U A 5 0.07 SIDE CHAIN
REMARK 500 4 C A 7 0.07 SIDE CHAIN
REMARK 500 4 A A 9 0.08 SIDE CHAIN
REMARK 500 4 G A 10 0.07 SIDE CHAIN
REMARK 500 4 U A 14 0.17 SIDE CHAIN
REMARK 500 4 C A 17 0.14 SIDE CHAIN
REMARK 500 4 U A 18 0.16 SIDE CHAIN
REMARK 500 4 U A 19 0.06 SIDE CHAIN
REMARK 500 5 C A 3 0.08 SIDE CHAIN
REMARK 500 5 C A 4 0.08 SIDE CHAIN
REMARK 500 5 U A 5 0.06 SIDE CHAIN
REMARK 500 5 A A 9 0.07 SIDE CHAIN
REMARK 500 5 U A 14 0.15 SIDE CHAIN
REMARK 500 5 C A 17 0.20 SIDE CHAIN
REMARK 500 5 U A 18 0.08 SIDE CHAIN
REMARK 500 6 C A 4 0.07 SIDE CHAIN
REMARK 500 6 A A 9 0.06 SIDE CHAIN
REMARK 500 6 U A 14 0.22 SIDE CHAIN
REMARK 500 6 C A 17 0.18 SIDE CHAIN
REMARK 500 6 U A 18 0.11 SIDE CHAIN
REMARK 500 7 U A 5 0.17 SIDE CHAIN
REMARK 500 7 C A 6 0.11 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 180 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2IXZ RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE APICAL STEM-LOOP OF THE HUMAN HEPATITIS B
REMARK 900 VIRUS ENCAPSIDATION SIGNAL
DBREF 2IXY A 1 27 PDB 2IXY 2IXY 1 27
SEQRES 1 A 27 G G C C U C C A A G C U G
SEQRES 2 A 27 U G C C U U G G G U G G C
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
MODEL 1
Complete list - y 9 2 Bytes