10 20 30 40 50 60 70 80 1DHH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA-RNA HYBRID 18-OCT-95 1DHH
TITLE NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA TITLE 2 HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*GP*G)-R(P*AP*GP*AP*U)- COMPND 3 D(P*GP*AP*C)-3'); COMPND 4 CHAIN: A; COMPND 5 SYNONYM: DHD; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, COMPND 8 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3'); COMPND 11 CHAIN: B; COMPND 12 SYNONYM: DHD; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, COMPND 15 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: A SUBSTRATE OF RNASE H; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: A SUBSTRATE OF RNASE H
KEYWDS NMR, DNA/RNA HYBRID IN DNA DUPLEX, DNA-RNA HYBRID
EXPDTA SOLUTION NMR
AUTHOR T.NISHIZAKI,S.IWAI,T.OHKUBO,C.KOJIMA,H.NAKAMURA,Y.KYOGOKU, AUTHOR 2 E.OHTSUKA
REVDAT 3 24-FEB-09 1DHH 1 VERSN REVDAT 2 01-APR-03 1DHH 1 JRNL REVDAT 1 03-APR-96 1DHH 0
JRNL AUTH T.NISHIZAKI,S.IWAI,T.OHKUBO,C.KOJIMA,H.NAKAMURA, JRNL AUTH 2 Y.KYOGOKU,E.OHTSUKA JRNL TITL SOLUTION STRUCUTRES OF DNA DUPLEXES CONTAINING A JRNL TITL 2 DNA X RNA HYBRID REGION, D(GG)R(AGAU)D(GAC) X JRNL TITL 3 D(GTCATCTCC) AND D(GGAGA)R(UGAC) X D(GTCATCTCC). JRNL REF BIOCHEMISTRY V. 35 4016 1996 JRNL REFN ISSN 0006-2960 JRNL PMID 8672435 JRNL DOI 10.1021/BI9519821
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1F REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RMSD BOND DISTANCES 0.0077 ANGSTROMS REMARK 3 RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN REMARK 3 REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID REMARK 3 ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS REMARK 3 0 THE STRUCTURES WAS REFINED BY A COMBINATION OF RESTRAINED REMARK 3 MOLECULAR DYNAMICS USING THE X-PLOR (V3.1F) PROGRAM (BRUNGER REMARK 3 1988) AND FULL RELAXATION MATRIX REFINEMENT OF THE TWO- REMARK 3 DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRUM AT 150 MSEC.
REMARK 4 REMARK 4 1DHH COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
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 : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL 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 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 A A 3 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 4 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 G A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 A A 5 C3' - C2' - C1' ANGL. DEV. = 5.0 DEGREES REMARK 500 A A 5 N7 - C8 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DG A 7 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DG A 7 N7 - C8 - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 DG A 7 C8 - N9 - C4 ANGL. DEV. = -2.4 DEGREES REMARK 500 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA A 8 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG B 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 4.3 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 A A 3 0.05 SIDE_CHAIN REMARK 500 U A 6 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DRN RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE
DBREF 1DHH A 1 9 PDB 1DHH 1DHH 1 9 DBREF 1DHH B 10 18 PDB 1DHH 1DHH 10 18
SEQRES 1 A 9 DG DG A G A U DG DA DC SEQRES 1 B 9 DG DT DC DA DT DC DT DC DC
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