4R6M | pdb_00004r6m

Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs

PDB DOI: https://doi.org/10.2210/pdb4R6M/pdb
NAKB: 4R6M

Classification: DNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2014-08-26 Released: 2015-09-02
Deposition Author(s): Xu, C.Y., Yu, F., Wang, L.H., Zhao, Y., Lin, T., Fan, C.H., He, J.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.240 (Depositor), 0.291 (DCC)
R-Value Work:
0.215 (Depositor)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs

Xu, C.Y., Yu, F., Wang, L.H., Zhao, Y., Lin, T., Fan, C.H., He, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 19.42 kDa
Atom Count: 1,242
Modeled Residue Count: 60
Deposited Residue Count: 60
Unique nucleic acid chains: 2

Macromolecules

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Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(PGPGPAPCPTPTPCPGPCPG)-3')	A, C, E	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(PCPGPCPGPTPTPGPTPCPC)-3')	B, D, F	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth D] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain L [auth F]	G [auth B] H [auth B] I [auth D] J [auth D] K [auth E] G [auth B], H [auth B], I [auth D], J [auth D], K [auth E], L [auth F]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.240 (Depositor), 0.291 (DCC)
R-Value Work: 0.215 (Depositor)
R-Value Observed: 0.217 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.785	α = 90
b = 70.785	β = 90
c = 108.037	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.