2D5K	Metal Binding Protein	date	Nov 02, 2005
title	Crystal Structure Of Dps From Staphylococcus Aureus
authors	Y.Tanaka, M.Yao, N.Watanabe, I.Tanaka
compound		source
Molecule: Dps Family Protein Chain: A, B, C, D Synonym: Dps Ec: 4.2.1.52 Engineered: Yes		Organism_scientific: Staphylococcus Aureus Subsp. Aureus Organism_taxid: 93062 Strain: Col Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: B834(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet28b
symmetry	Space Group: P 3 2 1	R_factor 0.190 R_Free 0.208
crystal cell	length a length b length c angle alpha angle beta angle gamma 143.381 143.381 88.288 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand	GOL	enzyme	Lyase E.C.4.2.1.52 BRENDA
Gene Ontology	Chain Function Process Component A, D, C, B
Primary reference	Nucleoid compaction by MrgA(Asp56Ala/Glu60Ala) does not contribute to staphylococcal cell survival against oxidative stress and phagocytic killing by macrophages., Ushijima Y, Ohniwa RL, Maruyama A, Saito S, Tanaka Y, Morikawa K, FEMS Microbiol Lett. 2014 Nov;360(2):144-51. doi: 10.1111/1574-6968.12598. Epub, 2014 Oct 21. PMID:25227518

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk] Biological Unit Coordinates (2d5k.pdb1.gz) 303 Kb LPC: Ligand-Protein Contacts for 2D5K CSU: Contacts of Structural Units for 2D5K Likely Quarternary Molecular Structure file(s) for 2D5K Structure Factors (712 Kb) Retrieve 2D5K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2D5K from S2C, [Save to disk] Re-refined 2d5k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2D5K in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 2D5K

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 2D5K, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2d5k_A] [2d5k_D] [2d5k] [2d5k_C] [2d5k_B] SWISS-PROT database: [Q5HE61] Domain organization of [Q5HE61_STAAC] by SWISSPFAM

Other resources with information on 2D5K

Community annotation for 2D5K at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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