HEADER DNA-RNA HYBRID 15-NOV-95 1DRN TITLE NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID TITLE 2 REGION, D(GGAGA)R(UGAC)/D(GTCATCTCC) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*GP*GP*AP*GP*A)-R(P*UP*GP*AP*C)-3'); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DDH; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, COMPND 7 50MM NA PHOSPHATE, 3MM EDTA; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3'); COMPND 10 CHAIN: B; COMPND 11 SYNONYM: DDH; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, COMPND 14 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 DOUBLE HELIX, DNA/RNA HYBRID, DNA-RNA HYBRID EXPDTA SOLUTION NMR AUTHOR T.NISHIZAKI,S.IWAI,T.OHKUBO,C.KOJIMA,H.NAKAMURA,Y.KYOGOKU,E.OHTSUKA REVDAT 4 16-FEB-22 1DRN 1 REMARK REVDAT 3 24-FEB-09 1DRN 1 VERSN REVDAT 2 01-APR-03 1DRN 1 JRNL REVDAT 1 03-APR-96 1DRN 0 JRNL AUTH T.NISHIZAKI,S.IWAI,T.OHKUBO,C.KOJIMA,H.NAKAMURA,Y.KYOGOKU, JRNL AUTH 2 E.OHTSUKA JRNL TITL SOLUTION STRUCUTRES OF DNA DUPLEXES CONTAINING A DNA X RNA JRNL TITL 2 HYBRID REGION, D(GG)R(AGAU)D(GAC) X D(GTCATCTCC) AND JRNL TITL 3 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 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: 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 0 REMARK 3 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 1DRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000172910. 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 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG A 1 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 1 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 DA A 3 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 3 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DG A 4 N7 - C8 - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 DG A 4 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 DA A 5 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DA A 5 N7 - C8 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 G A 7 C3' - C2' - C1' ANGL. DEV. = 5.2 DEGREES REMARK 500 G A 7 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 7 N7 - C8 - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 G A 7 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 A A 8 N7 - C8 - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 10 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 DG B 10 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 DG B 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 13 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 13 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT B 14 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 DC B 15 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC B 17 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DHH RELATED DB: PDB REMARK 900 MINIMIZED AVERAGE STRUCTURE DBREF 1DRN A 1 9 PDB 1DRN 1DRN 1 9 DBREF 1DRN B 10 18 PDB 1DRN 1DRN 10 18 SEQRES 1 A 9 DG DG DA DG DA U G A C 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