HEADER 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 SUPPORT SOURCE 4 USING PHOSPHORAMIDITE CHEMISTRY KEYWDS G-QUADRUPLEX, MONOVALENT CATIONS, DNA EXPDTA SOLUTION NMR NUMMDL 8 AUTHOR P.SKET,M.CRNUGELJ,J.PLAVEC REVDAT 3 02-MAR-22 1U64 1 REMARK 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 STRUCTURE WITH JRNL TITL 2 THE SAME GENERAL FOLD IN THE PRESENCE OF K+, NA+ OR NH4+ JRNL TITL 3 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 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, AMBER 7 REMARK 3 AUTHORS : VARIAN (VNMR), KOLLMAN, AT ALL (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 414 NOE-DERIVED DISTANCE RESTRAINTS REMARK 3 ASSOCIATED WITH THE NONEXCHANGEABLE AND EXCHANGEABLE PROTONS; 24 REMARK 3 HYDROGEN-BOND RESTRAINTS; 66 TORSION ANGLE RESTRAINTS FOR SUGAR REMARK 3 MOIETIES. FOR EACH OF FIVE DIFFERENT INITIAL STRUCTURES TEN REMARK 3 SIMULATED ANNEALING CALCULATIONS AT 700 K WITH NMR RESTRAINTS REMARK 3 USING A GENERALIZED BORN (GB) IMPLICIT SOLVATION MODEL WERE REMARK 3 PERFORMED FOR 60 PS. THE RESULTING STRUCTURES WERE SUBJECTED TO REMARK 3 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 02-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023292. 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% H2O, REMARK 210 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 : 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, STRUCTURES REMARK 210 WITH THE LOWEST 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 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 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. = -4.2 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. = 4.2 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 MODEL 1