Header list of 1hg9.pdb file
Complete list - t 9 2 Bytes
HEADER DNA-RNA HYBRID 13-DEC-00 1HG9
TITLE SOLUTION STRUCTURE OF DNA:RNA HYBRID
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5- D(*CP*TP*GP*AP*TP*AP*TP*GP*C) -3;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5- R(*GP*CP*AP*UP*AP*UP*CP*AP*G) -3;
COMPND 7 CHAIN: B;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 4 ORGANISM_TAXID: 32630;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 8 ORGANISM_TAXID: 32630
KEYWDS DNA-RNA HYBRID, DNA RNA HYBRID, DNA/RNA CHIMERIC HYBRID DUPLEX,
KEYWDS 2 ANTISENSE, LOCKED NUCLEIC ACID, DNA, RNA, HYBRID, RNASE H
EXPDTA SOLUTION NMR
NUMMDL 40
AUTHOR M.PETERSEN,K.BONDENSGAARD,J.WENGEL,J.P.JACOBSEN
REVDAT 4 09-OCT-19 1HG9 1 SOURCE JRNL REMARK
REVDAT 3 24-FEB-09 1HG9 1 VERSN
REVDAT 2 30-MAY-02 1HG9 1 REMARK
REVDAT 1 02-JAN-02 1HG9 0
JRNL AUTH K.BONDENSGAARD,M.PETERSEN,S.K.SINGH,V.K.RAJWANSHI,R.KUMAR,
JRNL AUTH 2 J.WENGEL,J.P.JACOBSEN
JRNL TITL STRUCTURAL STUDIES OF LNA:RNA DUPLEXES BY NMR: CONFORMATIONS
JRNL TITL 2 AND IMPLICATIONS FOR RNASE H ACTIVITY.
JRNL REF CHEMISTRY V. 6 2687 2000
JRNL REFN ISSN 0947-6539
JRNL PMID 10985717
JRNL DOI 10.1002/1521-3765(20000804)6:15<2687::AID-CHEM2687>3.0.CO;2-
JRNL DOI 2 U
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH M.PETERSEN,C.B.NIELSEN,K.E.NIELSEN,G.A.JENSEN,
REMARK 1 AUTH 2 K.BONDENSGAARD,S.K.SINGH,V.K.RAJWANSHI,A.A.KOSHKIN,B.M.DAHL,
REMARK 1 AUTH 3 J.WENGEL,J.P.JACOBSEN
REMARK 1 TITL THE CONFORMATIONS OF LOCKED NUCLEIC ACIDS (LNA)
REMARK 1 REF J.MOL.RECOGNIT. V. 13 44 2000
REMARK 1 REFN ISSN 0952-3499
REMARK 1 PMID 10679896
REMARK 1 DOI 10.1002/(SICI)1099-1352(200001/02)13:1<44::AID-JMR486>3.0.CO
REMARK 1 REFERENCE 2
REMARK 1 AUTH M.PETERSEN,K.BONDENSGAARD,J.WENGEL,J.P.JACOBSEN
REMARK 1 TITL LOCKED NUCLEIC ACID (LNA) RECOGNITION OF RNA: NMR SOLUTION
REMARK 1 TITL 2 STRUCTURES OF LNA:RNA HYBRIDS
REMARK 1 REF J.AM.CHEM.SOC. V. 124 5974 2002
REMARK 1 REFN ISSN 0002-7863
REMARK 1 PMID 12022830
REMARK 1 DOI 10.1021/JA012288D
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER
REMARK 3 AUTHORS : CASE, DA, KOLLMAN, PA
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 354 NOE DISTANCE RESTRAINTS
REMARK 3 WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE
REMARK 3 PROGRAM RANDMARDI. 22 WATSON-CRICK BASE PAIRING RESTRAINTS.
REMARK 4
REMARK 4 1HG9 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-00.
REMARK 100 THE DEPOSITION ID IS D_1290005661.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : 0.1
REMARK 210 PRESSURE : 1 ATM
REMARK 210 SAMPLE CONTENTS : 2.0E-3M DNA:RNA, 0.1M NACL, 5E
REMARK 210 -5M EDTA AND 1E-2M PHOSPHATE
REMARK 210 BUFFER IN 100% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ
REMARK 210 SPECTROMETER MODEL : INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : MARDIGRAS, AMBER, FELIX
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 40
REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 20
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: 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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
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 15 G B 10 C2' G B 10 C1' -0.048
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 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 1 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.3 DEGREES
REMARK 500 1 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 1 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES
REMARK 500 1 DG A 8 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES
REMARK 500 1 DG A 8 C5' - C4' - O4' ANGL. DEV. = 6.9 DEGREES
REMARK 500 1 DG A 8 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES
REMARK 500 1 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES
REMARK 500 1 A B 12 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 A B 12 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES
REMARK 500 1 U B 13 C5' - C4' - O4' ANGL. DEV. = 6.5 DEGREES
REMARK 500 1 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 C B 16 O4' - C1' - N1 ANGL. DEV. = 8.5 DEGREES
REMARK 500 1 A B 17 C5' - C4' - O4' ANGL. DEV. = 11.6 DEGREES
REMARK 500 1 G B 18 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES
REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 2 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.4 DEGREES
REMARK 500 2 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 2 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES
REMARK 500 2 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES
REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES
REMARK 500 2 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 2 DG A 8 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES
REMARK 500 2 DG A 8 C1' - O4' - C4' ANGL. DEV. = -6.8 DEGREES
REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES
REMARK 500 2 G B 10 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES
REMARK 500 2 G B 10 C5' - C4' - C3' ANGL. DEV. = -10.3 DEGREES
REMARK 500 2 G B 10 C1' - O4' - C4' ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 C B 11 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 2 A B 12 C3' - C2' - C1' ANGL. DEV. = -6.8 DEGREES
REMARK 500 2 A B 12 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES
REMARK 500 2 U B 13 C5' - C4' - O4' ANGL. DEV. = 6.0 DEGREES
REMARK 500 2 U B 15 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 C B 16 O4' - C1' - N1 ANGL. DEV. = 8.2 DEGREES
REMARK 500 2 A B 17 C5' - C4' - O4' ANGL. DEV. = 11.2 DEGREES
REMARK 500 2 G B 18 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES
REMARK 500 3 DC A 1 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES
REMARK 500 3 DT A 2 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES
REMARK 500 3 DT A 2 C6 - C5 - C7 ANGL. DEV. = -4.2 DEGREES
REMARK 500 3 DA A 4 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES
REMARK 500 3 DT A 5 O4' - C4' - C3' ANGL. DEV. = 4.6 DEGREES
REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES
REMARK 500 3 DG A 8 O4' - C4' - C3' ANGL. DEV. = 4.5 DEGREES
REMARK 500 3 DG A 8 C5' - C4' - O4' ANGL. DEV. = 7.7 DEGREES
REMARK 500 3 DG A 8 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES
REMARK 500 3 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES
REMARK 500 3 C B 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 3 A B 12 C3' - C2' - C1' ANGL. DEV. = -6.4 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 850 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 DT A 2 0.08 SIDE CHAIN
REMARK 500 1 DC A 9 0.13 SIDE CHAIN
REMARK 500 1 G B 10 0.08 SIDE CHAIN
REMARK 500 1 A B 12 0.08 SIDE CHAIN
REMARK 500 1 A B 14 0.11 SIDE CHAIN
REMARK 500 1 U B 15 0.11 SIDE CHAIN
REMARK 500 1 A B 17 0.09 SIDE CHAIN
REMARK 500 1 G B 18 0.08 SIDE CHAIN
REMARK 500 2 DT A 2 0.07 SIDE CHAIN
REMARK 500 2 DC A 9 0.14 SIDE CHAIN
REMARK 500 2 G B 10 0.08 SIDE CHAIN
REMARK 500 2 A B 12 0.09 SIDE CHAIN
REMARK 500 2 A B 14 0.13 SIDE CHAIN
REMARK 500 2 U B 15 0.11 SIDE CHAIN
REMARK 500 2 A B 17 0.10 SIDE CHAIN
REMARK 500 2 G B 18 0.07 SIDE CHAIN
REMARK 500 3 DT A 2 0.08 SIDE CHAIN
REMARK 500 3 DC A 9 0.14 SIDE CHAIN
REMARK 500 3 G B 10 0.08 SIDE CHAIN
REMARK 500 3 C B 11 0.09 SIDE CHAIN
REMARK 500 3 A B 12 0.07 SIDE CHAIN
REMARK 500 3 U B 13 0.06 SIDE CHAIN
REMARK 500 3 A B 14 0.11 SIDE CHAIN
REMARK 500 3 U B 15 0.11 SIDE CHAIN
REMARK 500 3 A B 17 0.08 SIDE CHAIN
REMARK 500 3 G B 18 0.08 SIDE CHAIN
REMARK 500 4 DT A 2 0.07 SIDE CHAIN
REMARK 500 4 DC A 9 0.14 SIDE CHAIN
REMARK 500 4 G B 10 0.08 SIDE CHAIN
REMARK 500 4 A B 12 0.08 SIDE CHAIN
REMARK 500 4 A B 14 0.11 SIDE CHAIN
REMARK 500 4 U B 15 0.10 SIDE CHAIN
REMARK 500 4 A B 17 0.09 SIDE CHAIN
REMARK 500 4 G B 18 0.07 SIDE CHAIN
REMARK 500 5 DT A 2 0.07 SIDE CHAIN
REMARK 500 5 DC A 9 0.14 SIDE CHAIN
REMARK 500 5 G B 10 0.09 SIDE CHAIN
REMARK 500 5 C B 11 0.07 SIDE CHAIN
REMARK 500 5 A B 12 0.09 SIDE CHAIN
REMARK 500 5 A B 14 0.12 SIDE CHAIN
REMARK 500 5 U B 15 0.11 SIDE CHAIN
REMARK 500 5 A B 17 0.10 SIDE CHAIN
REMARK 500 5 G B 18 0.07 SIDE CHAIN
REMARK 500 6 DT A 2 0.07 SIDE CHAIN
REMARK 500 6 DC A 9 0.14 SIDE CHAIN
REMARK 500 6 G B 10 0.08 SIDE CHAIN
REMARK 500 6 A B 12 0.09 SIDE CHAIN
REMARK 500 6 A B 14 0.12 SIDE CHAIN
REMARK 500 6 U B 15 0.10 SIDE CHAIN
REMARK 500 6 A B 17 0.09 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 296 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HHW RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF LNA1:RNA HYBRID
REMARK 900 RELATED ID: 1HHX RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF LNA3:RNA HYBRID
DBREF 1HG9 A 1 9 PDB 1HG9 1HG9 1 9
DBREF 1HG9 B 10 18 PDB 1HG9 1HG9 10 18
SEQRES 1 A 9 DC DT DG DA DT DA DT DG DC
SEQRES 1 B 9 G C A U A U C A G
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 - t 9 2 Bytes