HEADER DNA 17-OCT-97 1AXP TITLE DNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 6 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC)); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DR10.DY10; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: DNA (D(GAAGAGAAGC)(DOT)D(GCTTCTCTTC)); COMPND 8 CHAIN: B; COMPND 9 SYNONYM: DR10.DY10; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS DNA DUPLEX, PURINE/PYRIMIDINE-RICH STRANDS, B-FORM, DEOXYRIBONUCLEIC KEYWDS 2 ACID, DNA EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR J.I.GYI,A.N.LANE,G.L.CONN,T.BROWN REVDAT 4 22-MAY-24 1AXP 1 REMARK REVDAT 3 16-FEB-22 1AXP 1 REMARK REVDAT 2 24-FEB-09 1AXP 1 VERSN REVDAT 1 22-APR-98 1AXP 0 JRNL AUTH J.I.GYI,A.N.LANE,G.L.CONN,T.BROWN JRNL TITL SOLUTION STRUCTURES OF DNA.RNA HYBRIDS WITH PURINE-RICH AND JRNL TITL 2 PYRIMIDINE-RICH STRANDS: COMPARISON WITH THE HOMOLOGOUS DNA JRNL TITL 3 AND RNA DUPLEXES. JRNL REF BIOCHEMISTRY V. 37 73 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9425027 JRNL DOI 10.1021/BI9719713 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.I.GYI,G.L.CONN,A.N.LANE,T.BROWN REMARK 1 TITL COMPARISON OF THE THERMODYNAMIC STABILITIES AND SOLUTION REMARK 1 TITL 2 CONFORMATIONS OF DNA.RNA HYBRIDS CONTAINING PURINE-RICH AND REMARK 1 TITL 3 PYRIMIDINE-RICH STRANDS WITH DNA AND RNA DUPLEXES REMARK 1 REF BIOCHEMISTRY V. 35 12538 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : MOLECULAR SIMULATIONS INC. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DISTANCE CONSTRAINTS FOR GLYCOSIDIC REMARK 3 TORSION ANGLES, DEOXYRIBOSE PSEUDOROTATIONAL PHASE ANGLES AND REMARK 3 AMPLITUDES CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING REMARK 3 CONSTANTS BY A LEAST SQUARES/GRID-SEARCH METHOD IMPLEMENTED IN REMARK 3 NUCFIT AND PFIT (A.N. LANE, NIMR, UK). INTERNUCLEOTIDE DISTANCE REMARK 3 CONSTRAINTS CALCULATED FROM NOE BUILD-UP CURVES. STRUCTURES REMARK 3 CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER REMARK 3 95.0 USING AN AMBER FORCEFIELD AND A DISTANCE DEPENDENT REMARK 3 DIELECTRIC CONSTANT. REMARK 4 REMARK 4 1AXP 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_1000171383. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 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 : NOESY; 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 : FELIX 95.0, NUCFIT, PFIT, REMARK 210 DISCOVER 95.0 (INSIGHT II) II) REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 32 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST POTENTIAL ENERGY AND REMARK 210 MINIMAL VIOLATIONS AND REMARK 210 ACCEPTABLE STEREOCHEMISTRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE ASSIGNMENTS, NOES AND COUPLING CONSTANTS DETERMINED REMARK 210 FROM 2D HOMONUCLEAR NMR EXPERIMENTS USING UNLABELLED SAMPLE. 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 1 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 1 DA A 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 1 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 1 DC B 7 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 1 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 2 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DA A 8 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DC A 10 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 3 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 2 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC B 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 2 DT B 8 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 2 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 2 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 3 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 3 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 3 DG A 4 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 DA A 5 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DG A 6 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DA A 7 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 3 DG A 9 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 DC B 5 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 3 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 3 DC B 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 3 DC B 10 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 4 DA A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 4 DG A 4 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 4 DA A 8 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 4 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DT B 4 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 4 DC B 5 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 4 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 83 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 3 DG A 1 0.08 SIDE CHAIN REMARK 500 4 DG B 1 0.05 SIDE CHAIN REMARK 500 4 DT B 3 0.07 SIDE CHAIN REMARK 500 5 DG B 1 0.05 SIDE CHAIN REMARK 500 5 DT B 9 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1AXP A 1 10 PDB 1AXP 1AXP 1 10 DBREF 1AXP B 1 10 PDB 1AXP 1AXP 1 10 SEQRES 1 A 10 DG DA DA DG DA DG DA DA DG DC SEQRES 1 B 10 DG DC DT DT DC DT DC DT DT 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 MODEL 1