HEADER DNA-RNA HYBRID 11-JAN-00 1DXN TITLE THE SOLUTION STRUCTURE OF [D(CGC)R(AAA)D(TTTGCG)]2: HYBRID JUNCTIONS TITLE 2 FLANKED BY DNA DUPLEXES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-D(*CP*GP*CP)-R(*AP*AP*AP)-D(*TP*TP*TP*GP*CP*G)- COMPND 3 3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS DNA-RNA HYBRID, DNA/RNA CHIMERIC HYBRID DUPLEX, DNA/RNA HYBRID, KEYWDS 2 CHIMERIC DUPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.-T.HSU,M.-T.CHOU,J.-W.CHENG REVDAT 4 15-JAN-20 1DXN 1 REMARK REVDAT 3 24-FEB-09 1DXN 1 VERSN REVDAT 2 19-JUL-00 1DXN 1 ATOM REVDAT 1 11-APR-00 1DXN 0 JRNL AUTH S.-T.HSU,M.-T.CHOU,S.-H.CHOU,W.-C.HUANG,J.-W.CHENG JRNL TITL HYDRATION OF [D(CGC)R(AAA)D(TTTGCG)]2 JRNL REF J.MOL.BIOL. V. 295 1129 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10653692 JRNL DOI 10.1006/JMBI.1999.3388 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DXN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1290004525. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 100% D2O OR 90% H2O:10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : THE STRUCTURE WAS DETERMINED REMARK 210 FROM 2D NMR SPECTROSCOPY WITH REMARK 210 UNLABELED SAMPLE REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SA, MD, MATRIX RELAXATION REMARK 210 REFINEMENT REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY 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 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 1 DG A 2 N7 DG A 2 C8 0.045 REMARK 500 1 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 1 DT A 8 C5 DT A 8 C7 0.044 REMARK 500 1 DG A 10 N7 DG A 10 C8 0.047 REMARK 500 1 DG A 12 N7 DG A 12 C8 0.045 REMARK 500 1 DC B 13 C3' DC B 13 C2' 0.088 REMARK 500 1 DG B 14 N7 DG B 14 C8 0.048 REMARK 500 1 DT B 19 C5 DT B 19 C7 0.042 REMARK 500 1 DT B 20 C5 DT B 20 C7 0.044 REMARK 500 1 DT B 21 C5 DT B 21 C7 0.037 REMARK 500 1 DG B 22 N7 DG B 22 C8 0.047 REMARK 500 1 DG B 24 N7 DG B 24 C8 0.043 REMARK 500 2 DC A 1 C3' DC A 1 C2' 0.082 REMARK 500 2 DG A 2 N7 DG A 2 C8 0.048 REMARK 500 2 DT A 7 C5 DT A 7 C7 0.043 REMARK 500 2 DT A 8 C5 DT A 8 C7 0.043 REMARK 500 2 DT A 9 C5 DT A 9 C7 0.037 REMARK 500 2 DG A 10 N7 DG A 10 C8 0.048 REMARK 500 2 DG A 12 N7 DG A 12 C8 0.041 REMARK 500 2 DC B 13 C3' DC B 13 C2' 0.087 REMARK 500 2 DG B 14 N7 DG B 14 C8 0.046 REMARK 500 2 DT B 19 C5 DT B 19 C7 0.045 REMARK 500 2 DT B 20 C5 DT B 20 C7 0.044 REMARK 500 2 DT B 21 C5 DT B 21 C7 0.037 REMARK 500 2 DG B 22 N7 DG B 22 C8 0.048 REMARK 500 2 DG B 24 N7 DG B 24 C8 0.043 REMARK 500 3 DC A 1 C3' DC A 1 C2' 0.088 REMARK 500 3 DG A 2 N7 DG A 2 C8 0.046 REMARK 500 3 DT A 7 C5 DT A 7 C7 0.043 REMARK 500 3 DT A 8 C5 DT A 8 C7 0.044 REMARK 500 3 DT A 9 C5 DT A 9 C7 0.037 REMARK 500 3 DG A 10 N7 DG A 10 C8 0.046 REMARK 500 3 DG A 12 N7 DG A 12 C8 0.044 REMARK 500 3 DC B 13 C3' DC B 13 C2' 0.081 REMARK 500 3 DG B 14 N7 DG B 14 C8 0.048 REMARK 500 3 A B 16 N7 A B 16 C8 0.044 REMARK 500 3 DT B 19 C5 DT B 19 C7 0.041 REMARK 500 3 DT B 20 C5 DT B 20 C7 0.044 REMARK 500 3 DT B 21 C5 DT B 21 C7 0.037 REMARK 500 3 DG B 22 N7 DG B 22 C8 0.046 REMARK 500 3 DG B 24 N7 DG B 24 C8 0.040 REMARK 500 4 DC A 1 C3' DC A 1 C2' 0.085 REMARK 500 4 DG A 2 N7 DG A 2 C8 0.048 REMARK 500 4 DT A 7 C5 DT A 7 C7 0.042 REMARK 500 4 DT A 8 C5 DT A 8 C7 0.043 REMARK 500 4 DG A 10 N7 DG A 10 C8 0.047 REMARK 500 4 DG A 12 N7 DG A 12 C8 0.043 REMARK 500 4 DC B 13 C3' DC B 13 C2' 0.080 REMARK 500 4 DG B 14 N7 DG B 14 C8 0.046 REMARK 500 4 DT B 19 C5 DT B 19 C7 0.043 REMARK 500 REMARK 500 THIS ENTRY HAS 133 BOND DEVIATIONS. 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. = 4.1 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DC A 3 N1 - C2 - O2 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 A A 4 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 A A 4 O4' - C1' - N9 ANGL. DEV. = 8.6 DEGREES REMARK 500 1 A A 6 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DT A 9 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 10 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG A 12 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 DG B 14 O4' - C1' - C2' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG B 14 C3' - O3' - P ANGL. DEV. = 8.2 DEGREES REMARK 500 1 DC B 15 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 A B 16 C1' - O4' - C4' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 A B 16 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 1 A B 18 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT B 19 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 DG B 22 O4' - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC B 23 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 DG B 24 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DC A 1 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DG A 2 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 DG A 2 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 DG A 2 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 2 DC A 3 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 A A 4 C1' - O4' - C4' ANGL. DEV. = -6.2 DEGREES REMARK 500 2 A A 4 O4' - C1' - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 2 A A 6 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 DT A 7 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 DT A 9 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DG A 10 O4' - C1' - C2' ANGL. DEV. = -6.6 DEGREES REMARK 500 2 DG A 10 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC B 13 N1 - C2 - O2 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 DG B 14 O4' - C1' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 2 DG B 14 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC B 15 N1 - C2 - O2 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 A B 16 C1' - O4' - C4' ANGL. DEV. = -5.8 DEGREES REMARK 500 2 A B 16 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 2 A B 18 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 2 DT B 19 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DT B 21 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 2 DG B 22 O4' - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 2 DG B 22 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DC B 23 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 264 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4618 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 4, 5, 6 IN CHAIN A AND 16, 17, 18 IN CHAIN B ARE REMARK 999 ARE RNA, THE REMAINING RESIDUES ARE ALL DNA DBREF 1DXN A 1 12 PDB 1DXN 1DXN 1 12 DBREF 1DXN B 13 24 PDB 1DXN 1DXN 13 24 SEQRES 1 A 12 DC DG DC A A A DT DT DT DG DC DG SEQRES 1 B 12 DC DG DC A A A DT DT DT DG DC DG 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