2DKF	Hydrolase	date	Apr 10, 2006
title	Crystal Structure Of Ttha0252 From Thermus Thermophilus Hb8, Degradation Protein Of The Metallo-Beta-Lactamase Superfami
authors	I.Ishikawa, N.Nakagawa, S.Kuramitsu, S.Yokoyama, R.Masui, Riken S Genomicsproteomics Initiative (Rsgi)
compound		source
Molecule: Metallo-Beta-Lactamase Superfamily Protein Chain: A, B, C, D Synonym: Ttha0252 Protein Engineered: Yes		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8 Gene: Ttha0252 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11a
symmetry	Space Group: C 1 2 1	R_factor 0.242 R_Free 0.285
crystal cell	length a length b length c angle alpha angle beta angle gamma 143.220 147.100 121.230 90.00 109.25 90.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	MSE, ZN	enzyme
Gene Ontology	Chain Function Process Component A, D, C, B nuclease activity endonuclease activity
Primary reference	Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily., Ishikawa H, Nakagawa N, Kuramitsu S, Masui R, J Biochem (Tokyo). 2006 Oct;140(4):535-42. Epub 2006 Aug 31. PMID:16945939

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (278 Kb) [Save to disk] Biological Unit Coordinates (2dkf.pdb1.gz) 72 Kb Biological Unit Coordinates (2dkf.pdb2.gz) 72 Kb Biological Unit Coordinates (2dkf.pdb3.gz) 71 Kb Biological Unit Coordinates (2dkf.pdb4.gz) 72 Kb Biological Unit Coordinates (2dkf.pdb5.gz) 138 Kb LPC: Ligand-Protein Contacts for 2DKF CSU: Contacts of Structural Units for 2DKF Likely Quarternary Molecular Structure file(s) for 2DKF Structure Factors (1042 Kb) Retrieve 2DKF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2DKF from S2C, [Save to disk] Re-refined 2dkf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2DKF in 3D

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Visual 3D analysis of 2DKF

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 2DKF, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2dkf_B] [2dkf_A] [2dkf_D] [2dkf] [2dkf_C] SWISS-PROT database: [Q5SLP1] Domain organization of [RNSE_THET8] by SWISSPFAM Domains found in 2DKF: [Beta-Casp] [Lactamase_B ] by SMART

Other resources with information on 2DKF

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

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