HEADER DNA 11-MAR-18 6FY6 TITLE CONCERTED DYNAMICS OF METALLO-BASE PAIRS IN AN A/B-FORM HELICAL TITLE 2 TRANSITION (MAJOR SPECIES) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*CP*GP*TP*CP*TP*CP*AP*TP*GP*AP*TP*AP*CP*G)-3') COMPND 3 _MAJOR; COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS METALLATED DUPLEX DNA, B-FORM HELIX, A-FORM HELIX, MERCURY(II)- KEYWDS 2 MEDIATED BASE PAIR, DNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.P.SCHMIDT,S.JURT,S.JOHANNSEN,A.KARIMI,R.K.O.SIGEL,N.W.LUEDTKE REVDAT 3 15-MAY-24 6FY6 1 LINK REVDAT 2 13-NOV-19 6FY6 1 JRNL REMARK REVDAT 1 09-OCT-19 6FY6 0 JRNL AUTH O.P.SCHMIDT,S.JURT,S.JOHANNSEN,A.KARIMI,R.K.O.SIGEL, JRNL AUTH 2 N.W.LUEDTKE JRNL TITL CONCERTED DYNAMICS OF METALLO-BASE PAIRS IN AN A/B-FORM JRNL TITL 2 HELICAL TRANSITION. JRNL REF NAT COMMUN V. 10 4818 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31645548 JRNL DOI 10.1038/S41467-019-12440-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.46 REMARK 3 AUTHORS : G. MARIUS CLORE , GUILLERMO BERMEJO, , JOHN REMARK 3 KUSZEWSKI, CHARLES D. SCHWIETERS, AND NICO TJANDRA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 2000 PRELIMINARY STRUCTURES WERE REMARK 3 CALCULATED. THE 20 LOWEST ENERGY STRUCTURES WERE SELECTED AND REMARK 3 SUBSEQUENTLY REFINED. OF THE 200 REFINED CONFORMERS CALCULATED REMARK 3 THE 20 LOWEST ENERGY STRUCTURES WERE CHOSEN REMARK 4 REMARK 4 6FY6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200008839. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 277; 298 REMARK 210 PH : 7.75; 7.35 REMARK 210 IONIC STRENGTH : 50; 50 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.4 MM POLYDEOXYRIBONUCLEOTIDE, REMARK 210 1.2 MM MERCURY (II) ION, 90% H2O/ REMARK 210 10% D2O; 0.4 MM REMARK 210 POLYDEOXYRIBONUCLEOTIDE, 1.2 MM REMARK 210 MERCURY (II) ION, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H COSY; REMARK 210 2D 1H-1H TOCSY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 4.0.0.B.16, XPLOR-NIH REMARK 210 2.46, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 102 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC A 4 N3 REMARK 620 2 DT B 25 N3 178.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HG A 101 HG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT A 11 N3 REMARK 620 2 DC B 18 N3 178.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HG A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HG A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34244 RELATED DB: BMRB REMARK 900 CONCERTED DYNAMICS OF METALLO-BASE PAIRS IN AN A/B-FORM HELICAL REMARK 900 TRANSITION (MAJOR SPECIES) REMARK 900 RELATED ID: 6FY7 RELATED DB: PDB REMARK 900 RELATED ID: 6RLS RELATED DB: PDB DBREF 6FY6 A 1 14 PDB 6FY6 6FY6 1 14 DBREF 6FY6 B 15 28 PDB 6FY6 6FY6 15 28 SEQRES 1 A 14 DC DG DT DC DT DC DA DT DG DA DT DA DC SEQRES 2 A 14 DG SEQRES 1 B 14 DC DG DT DC DT DC DA DT DG DA DT DA DC SEQRES 2 B 14 DG HET HG A 101 1 HET HG A 102 1 HETNAM HG MERCURY (II) ION FORMUL 3 HG 2(HG 2+) LINK N3 DC A 4 HG HG A 102 1555 1555 2.05 LINK N3 DT A 11 HG HG A 101 1555 1555 2.04 LINK HG HG A 101 N3 DC B 18 1555 1555 2.05 LINK HG HG A 102 N3 DT B 25 1555 1555 2.04 SITE 1 AC1 5 DA A 10 DT A 11 DA A 12 DC B 18 SITE 2 AC1 5 DT B 19 SITE 1 AC2 5 DC A 4 DT A 5 DA B 24 DT B 25 SITE 2 AC2 5 DA B 26 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