HEADER DNA 03-AUG-05 2AKG TITLE THALLIUM FORM OF THE G-QUADRUPLEX FROM OXYTRICHA NOVA, D(G4T4G4)2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SEQUENCE OBTAINED FROM STERKIELLA NOVA (OXYTRICHA SOURCE 4 NOVA) TELOMERE KEYWDS DEOXYRIBONUCLEIC ACID, G-QUADRUPLEX, THALLIUM, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.L.GILL,S.A.STROBEL,J.P.LORIA REVDAT 5 22-MAY-24 2AKG 1 REMARK REVDAT 4 09-MAR-22 2AKG 1 REMARK REVDAT 3 24-FEB-09 2AKG 1 VERSN REVDAT 2 06-DEC-05 2AKG 1 JRNL REVDAT 1 08-NOV-05 2AKG 0 JRNL AUTH M.L.GILL,S.A.STROBEL,J.P.LORIA JRNL TITL (205)TL NMR METHODS FOR THE CHARACTERIZATION OF MONOVALENT JRNL TITL 2 CATION BINDING TO NUCLEIC ACIDS JRNL REF J.AM.CHEM.SOC. V. 127 16723 2005 JRNL REFN ISSN 0002-7863 JRNL PMID 16305263 JRNL DOI 10.1021/JA055358F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, CNS 1.1 REMARK 3 AUTHORS : VARIAN, INC (VNMR), BRUNGER, ADAMS, CLORE, DELANO, REMARK 3 GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, REMARK 3 PANNU, READ, RICE, SIMONSON, WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AKG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-05. REMARK 100 THE DEPOSITION ID IS D_1000033999. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 278 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.005 M DNA, 0.0001 M EDTA-D12, REMARK 210 0.050 M THALLIUM-NITRATE, PH 6.0, REMARK 210 100% D2O; 0.005 M DNA, 0.0001 M REMARK 210 EDTA-D12, 0.050 M THALLIUM- REMARK 210 NITRATE, PH 6.0, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 31P-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY 3.110, CNS 1.1 REMARK 210 METHOD USED : (1) DISTANCE GEOMETRY WITH REMARK 210 SIMULATED ANNEALING; (2) TORSION REMARK 210 ANGLE DYNAMICS (2000 K FOR 60 PS REMARK 210 WITH 15 FS TIMESTEPS); (3) REMARK 210 CARTESIAN DYNAMICS (1000 K FOR 5 REMARK 210 PS WITH 5 FS TIMESTEPS); (4) REMARK 210 RESTRAINED MOLECULAR DYNAMICS REMARK 210 (100 CYCLES OF 200 STEPS EACH) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED WITHOUT THE USE OF REMARK 210 ISOTOPICALLY ENRICHED NUCLEOTIDES. 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 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 DG A 3 P DG A 3 OP1 -0.133 REMARK 500 1 DG A 3 P DG A 3 OP2 -0.129 REMARK 500 1 DT A 5 P DT A 5 OP1 -0.130 REMARK 500 1 DT A 5 P DT A 5 OP2 -0.133 REMARK 500 1 DG A 10 P DG A 10 OP1 -0.129 REMARK 500 1 DG A 10 P DG A 10 OP2 -0.133 REMARK 500 1 DG A 12 P DG A 12 OP1 -0.130 REMARK 500 1 DG A 12 P DG A 12 OP2 -0.133 REMARK 500 1 DG B 15 P DG B 15 OP1 -0.130 REMARK 500 1 DG B 15 P DG B 15 OP2 -0.133 REMARK 500 1 DT B 17 P DT B 17 OP1 -0.134 REMARK 500 1 DT B 17 P DT B 17 OP2 -0.130 REMARK 500 1 DG B 22 P DG B 22 OP1 -0.134 REMARK 500 1 DG B 22 P DG B 22 OP2 -0.130 REMARK 500 1 DG B 24 P DG B 24 OP1 -0.133 REMARK 500 1 DG B 24 P DG B 24 OP2 -0.129 REMARK 500 2 DG A 3 P DG A 3 OP1 -0.134 REMARK 500 2 DG A 3 P DG A 3 OP2 -0.129 REMARK 500 2 DT A 5 P DT A 5 OP1 -0.129 REMARK 500 2 DT A 5 P DT A 5 OP2 -0.134 REMARK 500 2 DG A 10 P DG A 10 OP1 -0.129 REMARK 500 2 DG A 10 P DG A 10 OP2 -0.132 REMARK 500 2 DG A 12 P DG A 12 OP1 -0.129 REMARK 500 2 DG A 12 P DG A 12 OP2 -0.133 REMARK 500 2 DG B 15 P DG B 15 OP1 -0.129 REMARK 500 2 DG B 15 P DG B 15 OP2 -0.134 REMARK 500 2 DT B 17 P DT B 17 OP1 -0.134 REMARK 500 2 DT B 17 P DT B 17 OP2 -0.129 REMARK 500 2 DG B 22 P DG B 22 OP1 -0.133 REMARK 500 2 DG B 22 P DG B 22 OP2 -0.128 REMARK 500 2 DG B 24 P DG B 24 OP1 -0.133 REMARK 500 2 DG B 24 P DG B 24 OP2 -0.129 REMARK 500 3 DG A 3 P DG A 3 OP1 -0.133 REMARK 500 3 DG A 3 P DG A 3 OP2 -0.130 REMARK 500 3 DT A 5 P DT A 5 OP1 -0.130 REMARK 500 3 DT A 5 P DT A 5 OP2 -0.133 REMARK 500 3 DG A 10 P DG A 10 OP1 -0.129 REMARK 500 3 DG A 10 P DG A 10 OP2 -0.132 REMARK 500 3 DG A 12 P DG A 12 OP1 -0.128 REMARK 500 3 DG A 12 P DG A 12 OP2 -0.133 REMARK 500 3 DG B 15 P DG B 15 OP1 -0.129 REMARK 500 3 DG B 15 P DG B 15 OP2 -0.133 REMARK 500 3 DT B 17 P DT B 17 OP1 -0.133 REMARK 500 3 DT B 17 P DT B 17 OP2 -0.131 REMARK 500 3 DG B 22 P DG B 22 OP1 -0.133 REMARK 500 3 DG B 22 P DG B 22 OP2 -0.128 REMARK 500 3 DG B 24 P DG B 24 OP1 -0.134 REMARK 500 3 DG B 24 P DG B 24 OP2 -0.128 REMARK 500 4 DG A 3 P DG A 3 OP1 -0.133 REMARK 500 4 DG A 3 P DG A 3 OP2 -0.129 REMARK 500 REMARK 500 THIS ENTRY HAS 160 BOND DEVIATIONS. 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 2 DT A 5 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 3 DT B 17 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 4 DG A 9 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 4 DT B 17 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 4 DG B 21 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 6 DG A 9 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 6 DG B 21 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 8 DT A 5 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 8 DT B 17 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 2AKG A 1 12 PDB 2AKG 2AKG 1 12 DBREF 2AKG B 13 24 PDB 2AKG 2AKG 13 24 SEQRES 1 A 12 DG DG DG DG DT DT DT DT DG DG DG DG SEQRES 1 B 12 DG 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