10 20 30 40 50 60 70 80 1A6H - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER 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, KEYWDS 2 D(CGG) TRIPLET REPEAT, GCGC TETRADS
EXPDTA SOLUTION NMR
NUMMDL 4
AUTHOR A.KETTANI,R.A.KUMAR,D.J.PATEL
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 JRNL TITL 2 THE 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 1
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 REMARK 3 OBTAINED USING METRIC MATRIX DISTANCE GEOMETRY, AND REMARK 3 SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS REMARK 3 USING A SET OF INTER-PROTON DISTANCES AND DIHEDRAL ANGLE REMARK 3 RESTRAINTS DERIVED FROM THE NMR DATA. THE FOUR DISTANCE- REMARK 3 REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION- REMARK 3 MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. ALL REMARK 3 CALCULATIONS WERE CARRIED OUT USING THE X-PLOR PROGRAM. THE REMARK 3 FINAL FOUR STRUCTURES WERE OBTAINED BY CONJUGATE GRADIENT REMARK 3 MINIMIZATION OF THE STRUCTURES OBTAINED BY RELAXATION MATRIX REMARK 3 BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE REMARK 3 UNWEIGHTED R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT. REMARK 3 THE R(1/6)-FACTOR IS DEFINED: R(1/6) = SUM{|I(OBS)^(1/6) - K* REMARK 3 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 REMARK 3 AND THE CALCULATED INTENSITIES, RESPECTIVELY. THE SUMMATIONS REMARK 3 RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSS PEAKS IN REMARK 3 NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 50, 100, REMARK 3 150, 200 AND 300 MS. EACH DNA STRAND FORMS A HAIR-PIN WITH THE REMARK 3 CENTRAL G-C BASES FORMING WATSON-CRICK BASE PAIRS. THE TWO REMARK 3 HAIR-PINS SHOW ANTIPARALLEL ALIGNMENT. THE NMR SPECTRA SHOW REMARK 3 ONLY ONE SET OF RESONANCES FOR THE TWO STRANDS. THEREFORE NON- REMARK 3 CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE IMPOSED ON ALL NON- REMARK 3 HYDROGEN ATOMS TO MAINTAIN THE TWO STRANDS SUPERIMPOSABLE. THE REMARK 3 MOLECULE EXHIBITS APPROXIMATE TWO-FOLD SYMMETRY. THE STRUCTURE REMARK 3 IS WELL-DEFINED AT RESIDUES G 1 - G 4, T 7 - G 11. RESIDUES T REMARK 3 5 AND T 6 ARE LESS 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 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; REMARK 210 COSY-90; TOCSY; (1)H-(31)P REMARK 210 COSY; (1H)-(13)C HMQC. NOESY REMARK 210 BUILDUP AT 50; 100; 150; 200 REMARK 210 AND 300 ; IN H(2)O: NOESY (80 REMARK 210 AND 250 MS); (1)H-(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- REMARK 210 PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY AND REMARK 210 RESTRAINED 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 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 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 DT A 6 C3' - O3' - P ANGL. DEV. = 9.0 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 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 DT B 6 C3' - O3' - P ANGL. DEV. = 9.1 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 DG A 8 C4' - C3' - C2' ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DT A 7 C3' - O3' - P ANGL. DEV. = 7.3 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