HEADER DNA 25-FEB-98 1A6H
TITLE DNA QUADRUPLEX CONTAINING GCGC TETRAD, NMR, 4 STRUCTURES
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DNA (5'-D(GP*CP*GP*GP*TP*TP*TP*GP*CP*GP*G)-3');
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS DEOXYRIBONUCLEIC ACID, DNA QUADRUPLEX, FRAGILE X SYNDROME, D(CGG)
KEYWDS 2 TRIPLET REPEAT, GCGC TETRADS, DNA
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR A.KETTANI,R.A.KUMAR,D.J.PATEL
REVDAT 5 22-MAY-24 1A6H 1 REMARK
REVDAT 4 16-FEB-22 1A6H 1 REMARK
REVDAT 3 19-MAY-09 1A6H 1 REMARK
REVDAT 2 24-FEB-09 1A6H 1 VERSN
REVDAT 1 17-JUN-98 1A6H 0
SPRSDE 17-JUN-98 1A6H 228D
JRNL AUTH A.KETTANI,R.A.KUMAR,D.J.PATEL
JRNL TITL SOLUTION STRUCTURE OF A DNA QUADRUPLEX CONTAINING THE
JRNL TITL 2 FRAGILE X SYNDROME TRIPLET REPEAT.
JRNL REF J.MOL.BIOL. V. 254 638 1995
JRNL REFN ISSN 0022-2836
JRNL PMID 7500339
JRNL DOI 10.1006/JMBI.1995.0644
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: A SET OF FOUR STRUCTURES WERE OBTAINED
REMARK 3 USING METRIC MATRIX DISTANCE GEOMETRY, AND SUBSEQUENTLY REFINED
REMARK 3 BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-
REMARK 3 PROTON DISTANCES AND DIHEDRAL ANGLE RESTRAINTS DERIVED FROM THE
REMARK 3 NMR DATA. THE FOUR DISTANCE-REFINED STRUCTURES WERE REFINED
REMARK 3 FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED
REMARK 3 MOLECULAR DYNAMICS. ALL CALCULATIONS WERE CARRIED OUT USING THE
REMARK 3 X-PLOR PROGRAM. THE FINAL FOUR STRUCTURES WERE OBTAINED BY
REMARK 3 CONJUGATE GRADIENT MINIMIZATION OF THE STRUCTURES OBTAINED BY
REMARK 3 RELAXATION MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR
REMARK 3 DYNAMICS. THE UNWEIGHTED R(1/6) VALUE WAS USED TO MONITOR THE
REMARK 3 REFINEMENT. THE R(1/6)-FACTOR IS DEFINED: R(1/6) = SUM{|I(OBS)^
REMARK 3 (1/6) - K*I(CALC)^(1/6)|} / SUM{I(OBS)^(1/6)}, WHERE K IS THE
REMARK 3 CALIBRATION FACTOR, AND I(OBS) AND I(CALC) ARE THE OBSERVED AND
REMARK 3 THE CALCULATED INTENSITIES, RESPECTIVELY. THE SUMMATIONS RUN
REMARK 3 THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSS PEAKS IN NOESY
REMARK 3 SPECTRA RECORDED IN D2O AND MIXING TIMES OF 50, 100, 150, 200
REMARK 3 AND 300 MS. EACH DNA STRAND FORMS A HAIR-PIN WITH THE CENTRAL G-
REMARK 3 C BASES FORMING WATSON-CRICK BASE PAIRS. THE TWO HAIR-PINS SHOW
REMARK 3 ANTIPARALLEL ALIGNMENT. THE NMR SPECTRA SHOW ONLY ONE SET OF
REMARK 3 RESONANCES FOR THE TWO STRANDS. THEREFORE NON-CRYSTALLOGRAPHIC
REMARK 3 SYMMETRY RESTRAINTS WERE IMPOSED ON ALL NON-HYDROGEN ATOMS TO
REMARK 3 MAINTAIN THE TWO STRANDS SUPERIMPOSABLE. THE MOLECULE EXHIBITS
REMARK 3 APPROXIMATE TWO-FOLD SYMMETRY. THE STRUCTURE IS WELL-DEFINED AT
REMARK 3 RESIDUES G 1 - G 4, T 7 - G 11. RESIDUES T 5 AND T 6 ARE LESS
REMARK 3 WELL DEFINED.
REMARK 4
REMARK 4 1A6H 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_1000170452.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 317
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : IN D(2)O: NOESY; COSY-45; COSY
REMARK 210 -90; TOCSY; (1)H-(31)P COSY; (1H)
REMARK 210 -(13)C HMQC. NOESY BUILDUP AT 50;
REMARK 210 100; 150; 200 AND 300 ; IN H(2)
REMARK 210 O: NOESY (80 AND 250 MS); (1)H-
REMARK 210 (15)N HMQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : VARIAN UNITY PLUS
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VARIAN VNMR VNMR, FELIX, X-PLOR
REMARK 210 METHOD USED : DISTANCE GEOMETRY AND RESTRAINED
REMARK 210 MOLECULAR DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 4
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4
REMARK 210 CONFORMERS, SELECTION CRITERIA : ALL CONFORMERS PRESENTED
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 H2' DG B 4 OP2 DT B 6 1.44
REMARK 500 H2' DG A 4 OP2 DT A 6 1.52
REMARK 500
REMARK 500 REMARK: NULL
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 DT A 5 C5 DT A 5 C7 0.037
REMARK 500 1 DT A 6 C5 DT A 6 C7 0.056
REMARK 500 1 DT A 7 C5' DT A 7 C4' 0.064
REMARK 500 1 DT B 5 C5 DT B 5 C7 0.039
REMARK 500 1 DT B 6 C5 DT B 6 C7 0.052
REMARK 500 1 DT B 7 C5' DT B 7 C4' 0.066
REMARK 500 2 DT A 5 C5 DT A 5 C7 0.039
REMARK 500 2 DT A 6 C5 DT A 6 C7 0.038
REMARK 500 2 DT A 7 C5' DT A 7 C4' 0.050
REMARK 500 2 DT B 5 C5 DT B 5 C7 0.040
REMARK 500 2 DT B 6 C5 DT B 6 C7 0.037
REMARK 500 2 DT B 7 C5' DT B 7 C4' 0.049
REMARK 500 3 DT A 5 C5 DT A 5 C7 0.038
REMARK 500 3 DT A 6 C5' DT A 6 C4' 0.042
REMARK 500 3 DT A 6 C5 DT A 6 C7 0.045
REMARK 500 3 DT B 5 C5 DT B 5 C7 0.038
REMARK 500 3 DT B 6 C5' DT B 6 C4' 0.042
REMARK 500 3 DT B 6 C5 DT B 6 C7 0.044
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. = 4.4 DEGREES
REMARK 500 1 DC A 2 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 DG A 3 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DG A 4 C3' - C2' - C1' ANGL. DEV. = 7.9 DEGREES
REMARK 500 1 DG A 4 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES
REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 DT A 6 C5' - C4' - C3' ANGL. DEV. = 10.3 DEGREES
REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 1 DT A 6 C4 - C5 - C7 ANGL. DEV. = 5.6 DEGREES
REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -7.4 DEGREES
REMARK 500 1 DT A 6 C3' - O3' - P ANGL. DEV. = 9.0 DEGREES
REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 2.5 DEGREES
REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.2 DEGREES
REMARK 500 1 DG A 8 C4' - C3' - C2' ANGL. DEV. = -5.0 DEGREES
REMARK 500 1 DC A 9 O4' - C1' - N1 ANGL. DEV. = -4.5 DEGREES
REMARK 500 1 DG B 1 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DC B 2 O4' - C1' - C2' ANGL. DEV. = -6.8 DEGREES
REMARK 500 1 DG B 3 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DG B 4 C3' - C2' - C1' ANGL. DEV. = 7.7 DEGREES
REMARK 500 1 DG B 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES
REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES
REMARK 500 1 DT B 6 C5' - C4' - C3' ANGL. DEV. = 10.3 DEGREES
REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.9 DEGREES
REMARK 500 1 DT B 6 C4 - C5 - C7 ANGL. DEV. = 5.4 DEGREES
REMARK 500 1 DT B 6 C6 - C5 - C7 ANGL. DEV. = -7.3 DEGREES
REMARK 500 1 DT B 6 C3' - O3' - P ANGL. DEV. = 9.1 DEGREES
REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES
REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES
REMARK 500 1 DG B 8 C4' - C3' - C2' ANGL. DEV. = -5.1 DEGREES
REMARK 500 1 DC B 9 O4' - C1' - N1 ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DC A 2 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES
REMARK 500 2 DG A 3 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DG A 4 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES
REMARK 500 2 DG A 4 O4' - C1' - N9 ANGL. DEV. = 8.9 DEGREES
REMARK 500 2 DT A 5 C4' - C3' - O3' ANGL. DEV. = 14.7 DEGREES
REMARK 500 2 DT A 5 O4' - C1' - C2' ANGL. DEV. = -7.2 DEGREES
REMARK 500 2 DT A 6 C5' - C4' - C3' ANGL. DEV. = 9.0 DEGREES
REMARK 500 2 DT A 6 C4 - C5 - C7 ANGL. DEV. = 5.5 DEGREES
REMARK 500 2 DT A 6 C6 - C5 - C7 ANGL. DEV. = -7.8 DEGREES
REMARK 500 2 DT A 7 C6 - C5 - C7 ANGL. DEV. = -5.3 DEGREES
REMARK 500 2 DT A 7 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES
REMARK 500 2 DG A 8 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES
REMARK 500 2 DC A 9 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES
REMARK 500 2 DG B 1 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES
REMARK 500 2 DC B 2 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES
REMARK 500 2 DG B 3 O4' - C1' - C2' ANGL. DEV. = -5.9 DEGREES
REMARK 500 2 DG B 4 C4' - C3' - C2' ANGL. DEV. = -4.5 DEGREES
REMARK 500 2 DG B 4 O4' - C1' - N9 ANGL. DEV. = 8.9 DEGREES
REMARK 500 2 DT B 5 C4' - C3' - O3' ANGL. DEV. = 14.7 DEGREES
REMARK 500
REMARK 500 THIS ENTRY HAS 118 ANGLE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 1A6H A 1 11 PDB 1A6H 1A6H 1 11
DBREF 1A6H B 1 11 PDB 1A6H 1A6H 1 11
SEQRES 1 A 11 DG DC DG DG DT DT DT DG DC DG DG
SEQRES 1 B 11 DG DC DG DG DT DT DT DG DC 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