HEADER DNA 29-APR-98 1BCE TITLE INTRAMOLECULAR TRIPLEX, NMR, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*AP*AP*GP*GP*AP*A)-3'); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: NON-NUCLEOTIDE LINKERS BETWEEN RESIDUES 6 AND 7 AND COMPND 6 BETWEEN 12 AND 13; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(*TP*TP*CP*CP*TP*T)-3'); COMPND 9 CHAIN: B, C; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: NON-NUCLEOTIDE LINKERS BETWEEN RESIDUES 6 AND 7 AND COMPND 12 BETWEEN 12 AND 13 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICAL SYNTHESIS; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS DEOXYRIBONUCLEIC ACID, DNA TRIPLEX, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR J.L.ASENSIO,T.BROWN,A.N.LANE REVDAT 5 22-MAY-24 1BCE 1 REMARK REVDAT 4 16-FEB-22 1BCE 1 REMARK REVDAT 3 24-FEB-09 1BCE 1 VERSN REVDAT 2 01-APR-03 1BCE 1 JRNL REVDAT 1 12-AUG-98 1BCE 0 JRNL AUTH J.L.ASENSIO,T.BROWN,A.N.LANE JRNL TITL COMPARISON OF THE SOLUTION STRUCTURES OF INTRAMOLECULAR DNA JRNL TITL 2 TRIPLE HELICES CONTAINING ADJACENT AND NON-ADJACENT CG.C+ JRNL TITL 3 TRIPLETS. JRNL REF NUCLEIC ACIDS RES. V. 26 3677 1998 JRNL REFN ISSN 0305-1048 JRNL PMID 9685482 JRNL DOI 10.1093/NAR/26.16.3677 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.L.ASENSIO,A.N.LANE,J.DHESI,S.BERGQVIST,T.BROWN REMARK 1 TITL THE CONTRIBUTION OF CYTOSINE PROTONATION TO THE STABILITY OF REMARK 1 TITL 2 PARALLEL DNA TRIPLE HELICES REMARK 1 REF J.MOL.BIOL. V. 275 811 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DISCOVER REMARK 3 AUTHORS : MSI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MD/SIMULATED ANNEALING REMARK 3 PROTOCOL REMARK 4 REMARK 4 1BCE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171586. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5 REMARK 210 IONIC STRENGTH : 0.1M REMARK 210 PRESSURE : 1 ATMOSPHERE REMARK 210 SAMPLE CONTENTS : H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DISCOVER REMARK 210 METHOD USED : RESTRAINED MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY, NMR R FACTORS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURES WERE BASED ON ANALYSIS OF SCALAR COUPLING REMARK 210 CONSTANTS AND DISTANCES DERIVED FROM TIME-DEPENDENT NOES USING REMARK 210 RESTRAINED MOLECULAR DYNAMICS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC C 15 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 2 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 6 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 2 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 2 DC C 15 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 3 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DC B 10 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 3 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DC C 15 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 3 DT C 17 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 DA A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DA A 6 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DC B 10 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DT C 13 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 4 DT C 14 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 4 DC C 15 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DC C 16 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DT C 18 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES REMARK 500 5 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 5 DA A 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 DC B 9 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 5 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DT B 12 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 5 DC C 15 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 DT C 17 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 5 DT C 18 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES REMARK 500 6 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 6 DA A 6 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 6 DT B 8 C6 - C5 - C7 ANGL. DEV. = -3.8 DEGREES REMARK 500 6 DC B 9 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 6 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 95 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BCB RELATED DB: PDB REMARK 900 ENSEMBLE OF 10 STRUCTURES REMARK 900 RELATED ID: 1BWG RELATED DB: PDB REMARK 900 ENSEMBLE OF 10 STRUCTURES DBREF 1BCE A 1 6 PDB 1BCE 1BCE 1 6 DBREF 1BCE B 7 12 PDB 1BCE 1BCE 7 12 DBREF 1BCE C 13 18 PDB 1BCE 1BCE 13 18 SEQRES 1 A 6 DA DA DG DG DA DA SEQRES 1 B 6 DT DT DC DC DT DT SEQRES 1 C 6 DT DT DC DC DT DT 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