HEADER DNA 27-MAR-98 1A8N TITLE SOLUTION STRUCTURE OF A NA+ CATION STABILIZED DNA TITLE 2 QUADRUPLEX CONTAINING G.G.G.G AND G.C.G.C TETRADS FORMED TITLE 3 BY G-G-G-C REPEATS OBSERVED IN AAV AND HUMAN CHROMOSOME 19, TITLE 4 NMR, 8 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA QUADRUPLEX CONTAINING G.G.G.G AND G.C.G.C COMPND 3 TETRADS; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: NA+ CATION STABILIZED SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS G-G-G-C REPEAT-CONTAINING DNA QUADRUPLEXES, G.G.G.G TETRADS, KEYWDS 2 G.C.G.C TETRADS, NA+ CATION COORDINATION SITES, KEYWDS 3 DEOXYRIBONUCLEIC ACID EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR A.KETTANI,S.BOUAZIZ,A.GORIN,H.ZHAO,R.JONES,D.J.PATEL REVDAT 3 24-FEB-09 1A8N 1 VERSN REVDAT 2 18-NOV-98 1A8N 1 COMPND REMARK TITLE JRNL REVDAT 2 2 1 KEYWDS HEADER REVDAT 1 14-OCT-98 1A8N 0 JRNL AUTH A.KETTANI,S.BOUAZIZ,A.GORIN,H.ZHAO,R.A.JONES, JRNL AUTH 2 D.J.PATEL JRNL TITL SOLUTION STRUCTURE OF A NA CATION STABILIZED DNA JRNL TITL 2 QUADRUPLEX CONTAINING G.G.G.G AND G.C.G.C TETRADS JRNL TITL 3 FORMED BY G-G-G-C REPEATS OBSERVED IN JRNL TITL 4 ADENO-ASSOCIATED VIRAL DNA. JRNL REF J.MOL.BIOL. V. 282 619 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9737926 JRNL DOI 10.1006/JMBI.1998.2030 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN REMARK 3 THE JRNL CITATION ABOVE REMARK 4 REMARK 4 1A8N 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) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 5 MM NACL, 0.2 MM NA2HPO4 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5 MM NACL, 0.2 MM NA2HPO4 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY, TOCSY, COSY-45, COSY REMARK 210 DQF REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : ACCEPTABLE COVALEN GEOMETRY, REMARK 210 LOW DISTANCE RESTRAINTS REMARK 210 VIOLATIONS AND FAVORABLE NON- REMARK 210 BONDED ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: 2D PROTON NOESY EXPERIMENTS IN D2O WERE PERFORMED AT REMARK 210 FIVE DIFFERENT MIXING TIMES (50, 100, 150, 200 AND 300 MS). 2D REMARK 210 PROTON NOESY EXPERIMENTS IN H2O WERE PERFORMED AT 80 AND 250 REMARK 210 MS. 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 6 C5 DT A 6 C7 0.046 REMARK 500 1 DT A 8 C5 DT A 8 C7 0.057 REMARK 500 1 DT B 6 C5 DT B 6 C7 0.041 REMARK 500 1 DT B 8 C5 DT B 8 C7 0.043 REMARK 500 2 DT A 6 C5 DT A 6 C7 0.036 REMARK 500 2 DT A 8 C5' DT A 8 C4' 0.050 REMARK 500 2 DT A 8 C5 DT A 8 C7 0.043 REMARK 500 2 DC A 12 C2' DC A 12 C1' 0.063 REMARK 500 2 DT B 8 C5' DT B 8 C4' 0.050 REMARK 500 2 DT B 8 C5 DT B 8 C7 0.051 REMARK 500 2 DC B 12 C2' DC B 12 C1' 0.064 REMARK 500 3 DT A 6 C5 DT A 6 C7 0.039 REMARK 500 3 DT A 8 C5' DT A 8 C4' 0.046 REMARK 500 3 DT A 8 C5 DT A 8 C7 0.051 REMARK 500 3 DT B 6 C5 DT B 6 C7 0.037 REMARK 500 3 DT B 8 C5' DT B 8 C4' 0.048 REMARK 500 3 DT B 8 C5 DT B 8 C7 0.046 REMARK 500 4 DT A 5 C5' DT A 5 C4' 0.047 REMARK 500 4 DT A 8 C5' DT A 8 C4' 0.045 REMARK 500 4 DT A 8 C5 DT A 8 C7 0.055 REMARK 500 4 DT B 5 C5' DT B 5 C4' 0.049 REMARK 500 4 DT B 8 C5' DT B 8 C4' 0.044 REMARK 500 4 DT B 8 C5 DT B 8 C7 0.055 REMARK 500 5 DT A 7 C5' DT A 7 C4' 0.048 REMARK 500 5 DT A 8 C5 DT A 8 C7 0.048 REMARK 500 5 DT B 6 C5 DT B 6 C7 0.036 REMARK 500 5 DT B 7 C5' DT B 7 C4' 0.047 REMARK 500 5 DT B 8 C5 DT B 8 C7 0.048 REMARK 500 6 DT A 8 C5 DT A 8 C7 0.040 REMARK 500 6 DC A 12 C2' DC A 12 C1' 0.061 REMARK 500 6 DT B 7 C5 DT B 7 C7 0.059 REMARK 500 6 DT B 8 C5 DT B 8 C7 0.041 REMARK 500 7 DT A 8 C5' DT A 8 C4' 0.043 REMARK 500 7 DT A 8 C5 DT A 8 C7 0.047 REMARK 500 7 DT B 6 C5 DT B 6 C7 0.040 REMARK 500 7 DT B 8 C5' DT B 8 C4' 0.044 REMARK 500 7 DT B 8 C5 DT B 8 C7 0.048 REMARK 500 8 DT A 8 C5 DT A 8 C7 0.049 REMARK 500 8 DT B 8 C5 DT B 8 C7 0.056 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' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG A 1 C1' - O4' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 DG A 2 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG A 2 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG A 2 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG A 3 O4' - C1' - C2' ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DG A 3 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 1 DC A 4 O4' - C4' - C3' ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC A 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC A 4 N3 - C4 - N4 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DC A 4 C5 - C4 - N4 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 DG A 3 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT A 5 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DC A 4 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT A 6 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DT A 6 C6 - C5 - C7 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DT A 5 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = -7.5 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DT A 8 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 1 DT A 8 C6 - C5 - C7 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DG A 10 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG A 11 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 1 DG A 11 C3' - C2' - C1' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DG B 1 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG B 1 C1' - O4' - C4' ANGL. DEV. = -6.9 DEGREES REMARK 500 1 DG B 2 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG B 2 C1' - O4' - C4' ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG B 2 O4' - C1' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG B 3 O4' - C1' - C2' ANGL. DEV. = -5.6 DEGREES REMARK 500 1 DG B 3 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 1 DC B 4 O4' - C4' - C3' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DC B 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DC B 4 N3 - C4 - N4 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC B 4 C5 - C4 - N4 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 DG B 3 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DT B 5 O4' - C1' - C2' ANGL. DEV. = -8.4 DEGREES REMARK 500 1 DT B 5 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 DT B 5 C6 - C5 - C7 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 DC B 4 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 1 DT B 6 P - O5' - C5' ANGL. DEV. = 9.9 DEGREES REMARK 500 1 DT B 6 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 1 DT B 6 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT B 5 C3' - O3' - P ANGL. DEV. = 8.7 DEGREES REMARK 500 1 DT B 7 O4' - C1' - N1 ANGL. DEV. = -7.3 DEGREES REMARK 500 1 DT B 7 C6 - C5 - C7 ANGL. DEV. = -4.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 470 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1A8N A 1 12 PDB 1A8N 1A8N 1 12 DBREF 1A8N B 1 12 PDB 1A8N 1A8N 1 12 SEQRES 1 A 12 DG DG DG DC DT DT DT DT DG DG DG DC SEQRES 1 B 12 DG DG DG DC DT DT DT DT DG DG DG 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 179 0 0 0 0 0 0 6 0 0 0 2 END