HEADER DNA 17-JAN-94 156D TITLE REFINED SOLUTION STRUCTURE OF THE DIMERIC QUADRUPLEX FORMED FROM THE TITLE 2 OXYTRICHA TELOMERIC OLIGONUCLEOTIDE D(GGGGTTTTGGGG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS DNA, QUADRUPLEX, OXYTRICHA TELOMERIC OLIGONUCLEOTIDE D(GGGGTTTTGGGG) EXPDTA SOLUTION NMR NUMMDL 8 MDLTYP MINIMIZED AVERAGE AUTHOR P.SCHULTZE,F.W.SMITH,J.FEIGON REVDAT 4 16-FEB-22 156D 1 REMARK REVDAT 3 07-APR-09 156D 1 REMARK REVDAT 2 24-FEB-09 156D 1 VERSN REVDAT 1 30-APR-94 156D 0 JRNL AUTH P.SCHULTZE,F.W.SMITH,J.FEIGON JRNL TITL REFINED SOLUTION STRUCTURE OF THE DIMERIC QUADRUPLEX FORMED JRNL TITL 2 FROM THE OXYTRICHA TELOMERIC OLIGONUCLEOTIDE JRNL TITL 3 D(GGGGTTTTGGGG). JRNL REF STRUCTURE V. 2 221 1994 JRNL REFN ISSN 0969-2126 JRNL PMID 8069635 JRNL DOI 10.1016/S0969-2126(00)00023-X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH F.W.SMITH,J.FEIGON REMARK 1 TITL STRAND ORIENTATION IN THE DNA QUADRUPLEX FORMED FROM THE REMARK 1 TITL 2 OXYTRICHA TELOMERE REPEAT OLIGONUCLEOTIDE D(G4T4G4) IN REMARK 1 TITL 3 SOLUTION REMARK 1 REF BIOCHEMISTRY V. 32 8682 1993 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.W.SMITH,J.FEIGON REMARK 1 TITL QUADRUPLEX STRUCTURE OF OXYTRICHA TELOMERIC DNA REMARK 1 TITL 2 OLIGONUCLEOTIDES REMARK 1 REF NATURE V. 356 164 1992 REMARK 1 REFN ISSN 0028-0836 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: REFINEMENT PROCEDURE STEP (1) REMARK 3 SUBSTRUCTURE EMBEDDING ON 20 STRUCTURES STEP (2) TEMPLATE REMARK 3 FITTING AND REGULARIZATION BY SIMULATED ANNEALING (20 STRUCTURES) REMARK 3 STEP (3) SIMULATED ANNEALING AND ENERGY MINIMIZATION (20 REMARK 3 STRUCTURES) STEP (4) RELAXATION MATRIX REFINEMENT ON THE BEST 8 REMARK 3 OF 20 STRUCTURES. THE DIMER POSSESSES A TWO-FOLD AXIS OF REMARK 3 SYMMETRY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW REMARK 3 WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN REMARK 3 APPLIED TO CHAIN A OF MODEL 1. THE COORDINATES OF THE ATOMS OF REMARK 3 CHAIN A TRANSFORMED IN THIS MANNER HAVE AN RMSD OF 0.0015 REMARK 3 ANGSTROMS FROM THE COORDINATES OF CHAIN B GIVEN IN THIS ENTRY. REMARK 4 REMARK 4 156D 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_1000170129. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : .05M 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 : SUBSTRUCTURE EMBEDDING, REMARK 210 SIMULATED ANNEALING, MATRIX REMARK 210 RELAXATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 3 C3' DG A 3 C2' -0.050 REMARK 500 1 DG A 3 C8 DG A 3 N9 -0.056 REMARK 500 1 DT A 6 C5 DT A 6 C6 -0.042 REMARK 500 1 DT A 6 C6 DT A 6 N1 -0.044 REMARK 500 1 DT A 8 C5 DT A 8 C7 0.037 REMARK 500 1 DG A 9 C3' DG A 9 C2' -0.052 REMARK 500 1 DG A 11 C8 DG A 11 N9 -0.072 REMARK 500 1 DG B 15 C3' DG B 15 C2' -0.049 REMARK 500 1 DG B 15 C8 DG B 15 N9 -0.055 REMARK 500 1 DT B 18 C5 DT B 18 C6 -0.043 REMARK 500 1 DT B 18 C6 DT B 18 N1 -0.046 REMARK 500 1 DT B 20 C5 DT B 20 C7 0.038 REMARK 500 1 DG B 21 C3' DG B 21 C2' -0.053 REMARK 500 1 DG B 23 C8 DG B 23 N9 -0.071 REMARK 500 2 DG A 3 C8 DG A 3 N9 -0.052 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.044 REMARK 500 2 DT A 8 C5 DT A 8 C7 0.037 REMARK 500 2 DG A 11 C4' DG A 11 C3' -0.062 REMARK 500 2 DG A 11 C8 DG A 11 N9 -0.060 REMARK 500 2 DG A 12 C5' DG A 12 C4' 0.044 REMARK 500 2 DG B 15 C8 DG B 15 N9 -0.052 REMARK 500 2 DT B 18 C5 DT B 18 C7 0.044 REMARK 500 2 DT B 20 C5 DT B 20 C7 0.036 REMARK 500 2 DG B 23 C4' DG B 23 C3' -0.063 REMARK 500 2 DG B 23 C8 DG B 23 N9 -0.060 REMARK 500 2 DG B 24 C5' DG B 24 C4' 0.045 REMARK 500 3 DG A 3 C8 DG A 3 N9 -0.060 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.066 REMARK 500 3 DT A 8 C6 DT A 8 N1 -0.044 REMARK 500 3 DG A 9 C8 DG A 9 N9 -0.044 REMARK 500 3 DG A 11 C4' DG A 11 C3' -0.063 REMARK 500 3 DG A 11 C8 DG A 11 N9 -0.053 REMARK 500 3 DG B 15 C8 DG B 15 N9 -0.060 REMARK 500 3 DT B 18 C5 DT B 18 C7 0.066 REMARK 500 3 DT B 19 C5 DT B 19 C7 0.037 REMARK 500 3 DT B 20 C6 DT B 20 N1 -0.044 REMARK 500 3 DG B 21 C8 DG B 21 N9 -0.042 REMARK 500 3 DG B 23 C4' DG B 23 C3' -0.062 REMARK 500 3 DG B 23 C8 DG B 23 N9 -0.054 REMARK 500 4 DG A 2 C2' DG A 2 C1' -0.065 REMARK 500 4 DG A 3 C3' DG A 3 C2' -0.063 REMARK 500 4 DG A 3 C8 DG A 3 N9 -0.065 REMARK 500 4 DG A 4 C3' DG A 4 C2' -0.054 REMARK 500 4 DG A 4 C2' DG A 4 C1' -0.064 REMARK 500 4 DT A 5 C4' DT A 5 C3' -0.063 REMARK 500 4 DT A 6 C3' DT A 6 C2' -0.058 REMARK 500 4 DT A 6 C5 DT A 6 C7 0.057 REMARK 500 4 DT A 8 C5 DT A 8 C7 0.047 REMARK 500 4 DG A 9 C8 DG A 9 N9 -0.048 REMARK 500 4 DG A 11 C4' DG A 11 C3' -0.085 REMARK 500 REMARK 500 THIS ENTRY HAS 109 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 DG A 1 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG A 2 C3' - C2' - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG A 2 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 2 N7 - C8 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 2 C8 - N9 - C4 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 3 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DG A 3 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 3 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 8.8 DEGREES REMARK 500 1 DT A 5 O4' - C4' - C3' ANGL. DEV. = 7.5 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DT A 5 C4 - C5 - C6 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DT A 5 C5 - C6 - N1 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DT A 6 C5' - C4' - O4' ANGL. DEV. = 8.1 DEGREES REMARK 500 1 DT A 6 O4' - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - C2' ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 1 DT A 7 C5 - C6 - N1 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DT A 8 O4' - C4' - C3' ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DT A 8 O4' - C1' - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 DG A 9 O4' - C4' - C3' ANGL. DEV. = 3.7 DEGREES REMARK 500 1 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 DG A 10 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG A 10 N7 - C8 - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 DG A 10 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 11 O4' - C4' - C3' ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG A 11 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 DG A 11 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DG A 11 C5 - N7 - C8 ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 11 N7 - C8 - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DG A 11 C8 - N9 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 DG A 12 C5' - C4' - O4' ANGL. DEV. = 13.3 DEGREES REMARK 500 1 DG A 12 C4' - C3' - C2' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DG A 12 O4' - C1' - C2' ANGL. DEV. = -11.4 DEGREES REMARK 500 1 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 DG A 12 C8 - N9 - C4 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 DG B 13 O4' - C1' - N9 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DG B 14 C3' - C2' - C1' ANGL. DEV. = 7.4 DEGREES REMARK 500 1 DG B 14 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG B 14 N7 - C8 - N9 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 DG B 15 O4' - C4' - C3' ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DG B 15 C5 - N7 - C8 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 DG B 15 N7 - C8 - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DG B 16 O4' - C1' - N9 ANGL. DEV. = 8.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 585 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 156D A 1 12 PDB 156D 156D 1 12 DBREF 156D B 13 24 PDB 156D 156D 13 24 SEQRES 1 A 12 DG DG DG DG DT DT DT DT DG DG DG DG SEQRES 1 B 12 DG DG DG DG DT DT DT DT DG DG DG 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