HEADER DNA 28-SEP-98 1BX5 TITLE NMR SOLUTION STRUCTURE OF [D(GCGAAT-3'-3'-ALPHAT-5'-5'-CGC)2] COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*CP*GP*AP*AP*TP*(ATD)P*CP*GP*C)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: ALPHA ANOMERIC THYMIDINES AT POSITION 7 3'-3' COMPND 7 PHOSPHODIESTER LINKAGE BETWEEN T6 AND ALPHAT7 5'-5' PHOSPHODIESTER COMPND 8 LINKAGE BETWEEN ALPHAT7 AND C8 SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS ALPHA ANOMERIC, POLARITY REVERSALS, DNA EXPDTA SOLUTION NMR AUTHOR J.M.ARAMINI,A.MUJEEB,M.W.GERMANN REVDAT 4 16-FEB-22 1BX5 1 REMARK LINK REVDAT 3 24-FEB-09 1BX5 1 VERSN REVDAT 2 22-DEC-99 1BX5 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 06-JAN-99 1BX5 0 JRNL AUTH J.M.ARAMINI,A.MUJEEB,M.W.GERMANN JRNL TITL NMR SOLUTION STRUCTURES OF JRNL TITL 2 [D(GCGAAT-3'-3'-ALPHAT-5'-5'-CGC)2] AND ITS UNMODIFIED JRNL TITL 3 CONTROL. JRNL REF NUCLEIC ACIDS RES. V. 26 5644 1998 JRNL REFN ISSN 0305-1048 JRNL PMID 9837995 JRNL DOI 10.1093/NAR/26.24.5644 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 4.1 REMARK 3 AUTHORS : PEARLMAN ET AL., 1995 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE REMARK 4 REMARK 4 1BX5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008176. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 MM NACL, 10 MM NAPHOSPHATE, REMARK 210 0.1 MM EDTA REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; DQF-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : RAMDMARDI, AMBER 4.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 9 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: REMARK 210 MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING DISTANCE AND REMARK 210 TORSION ANGLE REMARK 210 RESTRAINTS OBTAINED FROM HOMONUCLEAR NOESY (75, 150, 300 MS MIXING REMARK 210 TIMES) AND REMARK 210 DQF-COSY EXPERIMENTS. 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 DC A 2 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DC A 2 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 DG A 3 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 DA A 4 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DA A 5 O4' - C4' - C3' ANGL. DEV. = 3.9 DEGREES REMARK 500 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DT A 6 C4 - C5 - C7 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT A 6 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES REMARK 500 ATD A 7 O3' - P - O5' ANGL. DEV. = 46.7 DEGREES REMARK 500 DC A 8 O4' - C4' - C3' ANGL. DEV. = 5.7 DEGREES REMARK 500 DC A 8 C3' - C2' - C1' ANGL. DEV. = 10.6 DEGREES REMARK 500 DC A 8 O4' - C1' - N1 ANGL. DEV. = 10.8 DEGREES REMARK 500 DC A 10 O4' - C1' - N1 ANGL. DEV. = 4.1 DEGREES REMARK 500 DC B 12 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 DC B 12 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DG B 13 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DA B 15 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 DT B 16 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 DT B 16 C4 - C5 - C7 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT B 16 C6 - C5 - C7 ANGL. DEV. = -6.8 DEGREES REMARK 500 ATD B 17 O3' - P - O5' ANGL. DEV. = 46.6 DEGREES REMARK 500 DC B 18 O4' - C4' - C3' ANGL. DEV. = 5.6 DEGREES REMARK 500 DC B 18 C3' - C2' - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 DC B 18 O4' - C1' - N1 ANGL. DEV. = 9.9 DEGREES REMARK 500 DC B 20 O4' - C1' - N1 ANGL. DEV. = 4.2 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 DC A 8 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1BX5 A 1 10 PDB 1BX5 1BX5 1 10 DBREF 1BX5 B 11 20 PDB 1BX5 1BX5 11 20 SEQRES 1 A 10 DG DC DG DA DA DT ATD DC DG DC SEQRES 1 B 10 DG DC DG DA DA DT ATD DC DG DC MODRES 1BX5 ATD A 7 DT THYMIDINE-3'-PHOSPHATE MODRES 1BX5 ATD B 17 DT THYMIDINE-3'-PHOSPHATE HET ATD A 7 32 HET ATD B 17 32 HETNAM ATD THYMIDINE-3'-PHOSPHATE FORMUL 1 ATD 2(C10 H15 N2 O8 P) LINK O3' DT A 6 P ATD A 7 1555 1555 1.61 LINK O5' ATD A 7 P DC A 8 1555 1555 1.61 LINK O3' DT B 16 P ATD B 17 1555 1555 1.60 LINK O5' ATD B 17 P DC B 18 1555 1555 1.61 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