10 20 30 40 50 60 70 80 1U64 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER DNA 29-JUL-04 1U64
TITLE THE SOLUTION STRUCTURE OF D(G3T4G4)2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: G-RICH DNA OLIGOMER
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: OLIGOMER HAS BEEN PREPARED ON SOLID STATE SOURCE 4 SUPPORT USING PHOSPHORAMIDITE CHEMISTRY
KEYWDS G-QUADRUPLEX, NMR, MONOVALENT CATIONS, DNA
EXPDTA SOLUTION NMR
NUMMDL 8
AUTHOR P.SKET,M.CRNUGELJ,J.PLAVEC
REVDAT 2 24-FEB-09 1U64 1 VERSN REVDAT 1 26-OCT-04 1U64 0
JRNL AUTH P.SKET,M.CRNUGELJ,J.PLAVEC JRNL TITL D(G3T4G4) FORMS UNUSUAL DIMERIC G-QUADRUPLEX JRNL TITL 2 STRUCTURE WITH THE SAME GENERAL FOLD IN THE JRNL TITL 3 PRESENCE OF K+, NA+ OR NH4+ IONS. JRNL REF BIOORG.MED.CHEM. V. 12 5735 2004 JRNL REFN ISSN 0968-0896 JRNL PMID 15498650 JRNL DOI 10.1016/J.BMC.2004.08.009
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7 REMARK 3 AUTHORS : KOLLMAN, AT ALL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 414 NOE-DERIVED DISTANCE RESTRAINTS REMARK 3 ASSOCIATED WITH THE NONEXCHANGEABLE AND EXCHANGEABLE PROTONS; REMARK 3 24 HYDROGEN-BOND RESTRAINTS; 66 TORSION ANGLE RESTRAINTS FOR REMARK 3 SUGAR MOIETIES. FOR EACH OF FIVE DIFFERENT INITIAL STRUCTURES REMARK 3 TEN SIMULATED ANNEALING CALCULATIONS AT 700 K WITH NMR REMARK 3 RESTRAINTS USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION REMARK 3 MODEL WERE PERFORMED FOR 60 PS. THE RESULTING STRUCTURES WERE REMARK 3 SUBJECTED TO ENERGY MINIMIZATION
REMARK 4 REMARK 4 1U64 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-AUG-04. REMARK 100 THE RCSB ID CODE IS RCSB023292.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278; 298 REMARK 210 PH : 5.5; 5.5 REMARK 210 IONIC STRENGTH : 15MM KCL; 15MM KCL REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 4MM DG3T4G4 PER STRAND; 90% REMARK 210 H2O, 10% D2O, 15MM KCL; PH 5.5 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, PE-COSY, 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1B, FELIX 2000 REMARK 210 METHOD USED : SIMULATED ANNEALING, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR TECHNIQUES.
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 DG B 20 C6 DG B 20 N1 -0.043 REMARK 500 2 DG B 20 C6 DG B 20 N1 -0.044 REMARK 500 3 DG B 20 C6 DG B 20 N1 -0.043 REMARK 500 4 DG B 20 C6 DG B 20 N1 -0.043 REMARK 500 5 DG B 20 C6 DG B 20 N1 -0.042 REMARK 500 6 DG B 20 C6 DG B 20 N1 -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' - C2' ANGL. DEV. = 3.3 DEGREES REMARK 500 1 DG A 1 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 DG A 1 N3 - C4 - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 DG A 2 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 DT A 4 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DT A 4 C6 - C5 - C7 ANGL. DEV. = -3.7 DEGREES REMARK 500 1 DT A 5 O4' - C1' - N1 ANGL. DEV. = 7.0 DEGREES REMARK 500 1 DT A 6 O4' - C1' - N1 ANGL. DEV. = -6.6 DEGREES REMARK 500 1 DT A 6 N3 - C2 - O2 ANGL. DEV. = -4.5 DEGREES REMARK 500 1 DT A 7 O4' - C1' - N1 ANGL. DEV. = 5.7 DEGREES REMARK 500 1 DT A 7 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DT A 7 C6 - C5 - C7 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG A 8 O4' - C1' - N9 ANGL. DEV. = 1.8 DEGREES REMARK 500 1 DG A 10 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 1 DG A 11 O4' - C1' - N9 ANGL. DEV. = 8.0 DEGREES REMARK 500 1 DG B 12 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DG B 12 N3 - C2 - N2 ANGL. DEV. = -5.8 DEGREES REMARK 500 1 DG B 13 N3 - C2 - N2 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 DG B 14 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 1 DT B 16 C4 - C5 - C7 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 DT B 16 C6 - C5 - C7 ANGL. DEV. = -6.7 DEGREES REMARK 500 1 DT B 17 O4' - C1' - N1 ANGL. DEV. = 10.1 DEGREES REMARK 500 1 DT B 17 N3 - C2 - O2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DT B 18 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 DT B 18 N3 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 DG B 19 O4' - C4' - C3' ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG B 19 O4' - C1' - N9 ANGL. DEV. = 12.9 DEGREES REMARK 500 1 DG B 19 C6 - N1 - C2 ANGL. DEV. = -3.9 DEGREES REMARK 500 1 DG B 19 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 1 DG B 19 N1 - C2 - N2 ANGL. DEV. = 6.1 DEGREES REMARK 500 1 DG B 19 N3 - C2 - N2 ANGL. DEV. = -8.7 DEGREES REMARK 500 1 DG B 19 C5 - C6 - O6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 20 O4' - C1' - C2' ANGL. DEV. = -5.4 DEGREES REMARK 500 1 DG B 20 O4' - C1' - N9 ANGL. DEV. = 10.7 DEGREES REMARK 500 1 DG B 20 N3 - C4 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 DG B 20 N1 - C2 - N2 ANGL. DEV. = -9.4 DEGREES REMARK 500 1 DG B 20 N3 - C2 - N2 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DG B 20 N1 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 DG B 21 O4' - C1' - N9 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 DG B 22 O4' - C1' - C2' ANGL. DEV. = -4.9 DEGREES REMARK 500 1 DG B 22 O4' - C1' - N9 ANGL. DEV. = 12.5 DEGREES REMARK 500 1 DG B 22 C5 - C6 - O6 ANGL. DEV. = -4.1 DEGREES REMARK 500 2 DG A 1 O4' - C1' - C2' ANGL. DEV. = 3.5 DEGREES REMARK 500 2 DG A 1 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 2 DG A 1 N3 - C4 - C5 ANGL. DEV. = -3.5 DEGREES REMARK 500 2 DG A 1 N3 - C4 - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 DG A 2 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DT A 4 O4' - C1' - N1 ANGL. DEV. = 6.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 346 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL
DBREF 1U64 A 1 11 PDB 1U64 1U64 1 11 DBREF 1U64 B 12 22 PDB 1U64 1U64 12 22
SEQRES 1 A 11 DG DG DG DT DT DT DT DG DG DG DG SEQRES 1 B 11 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