HEADER DNA 22-MAY-19 6K3Y TITLE G-QUADRUPLEX COMPLEX WITH CYCLIC DINUCLEOTIDE 3'-3' CGAMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*TP*TP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*TP*GP*GP*GP*T)-3'); COMPND 4 CHAIN: A; COMPND 5 SYNONYM: DELTA1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS G-QUADRUPLEX, CGAMP, DINUCLEOTIDE, VACANCY, DNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.R.WINNERDY,B.HEDDI,A.T.PHAN REVDAT 2 14-JUN-23 6K3Y 1 HETSYN REVDAT 1 15-JAN-20 6K3Y 0 JRNL AUTH F.R.WINNERDY,P.DAS,B.HEDDI,A.T.PHAN JRNL TITL SOLUTION STRUCTURES OF A G-QUADRUPLEX BOUND TO LINEAR- AND JRNL TITL 2 CYCLIC-DINUCLEOTIDES. JRNL REF J.AM.CHEM.SOC. V. 141 18038 2019 JRNL REFN ESSN 1520-5126 JRNL PMID 31661272 JRNL DOI 10.1021/JACS.9B05642 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6K3Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300010070. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 283 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 30; 30 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM DELTA1, 1.5 MM CGAMP, 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 100% D2O; 1 REMARK 210 MM DELTA1, 1.5 MM CGAMP, 10 MM REMARK 210 POTASSIUM CHLORIDE, 10 MM REMARK 210 POTASSIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-13C HSQC ALIPHATIC; 2D 1H- REMARK 210 13C HSQC AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, X-PLOR NIH REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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: 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 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4BW A 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36253 RELATED DB: BMRB REMARK 900 G-QUADRUPLEX COMPLEX WITH CYCLIC DINUCLEOTIDE 3'-3' CGAMP DBREF 6K3Y A 1 17 PDB 6K3Y 6K3Y 1 17 SEQRES 1 A 17 DT DT DG DG DT DG DG DG DT DG DG DG DT SEQRES 2 A 17 DG DG DG DT HET 4BW A 101 67 HETNAM 4BW 2-AMINO-9-[(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-9- HETNAM 2 4BW (6-AMINO-9H-PURIN-9-YL)-3,5,10,12-TETRAHYDROXY-5,12- HETNAM 3 4BW DIOXIDOOCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9, HETNAM 4 4BW 2,8]TETRAOXADIPHOSPHACYCLODODECIN-2-YL]-1,9-DIHYDRO- HETNAM 5 4BW 6H-PURIN-6-ONE HETSYN 4BW 3',3' CGAMP; C-GMP-AMP; C[G(3',5')PA(3',5')P] FORMUL 2 4BW C20 H24 N10 O13 P2 SITE 1 AC1 5 DG A 4 DT A 5 DG A 8 DG A 16 SITE 2 AC1 5 DT A 17 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