3DZV | pdb_00003dzv

Crystal structure of 4-methyl-5-(beta-hydroxyethyl)thiazole kinase (NP_816404.1) from ENTEROCOCCUS FAECALIS V583 at 2.57 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DZV/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-30 Released: 2008-08-19 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of 4-methyl-5-(beta-hydroxyethyl)thiazole kinase (NP_816404.1) from ENTEROCOCCUS FAECALIS V583 at 2.57 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.5 kDa 
• Atom Count: 4,227 
• Modeled Residue Count: 530 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-methyl-5-(beta-hydroxyethyl)thiazole kinase	A, B	273	Enterococcus faecalis	Mutation(s): 0  Gene Names: NP_816404.1, EF_2777 EC: 2.7.1.50
UniProt
Find proteins for Q830K4 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830K4  Go to UniProtKB:  Q830K4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], H [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
SO4	C [auth A], D [auth A], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DZV

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.705	α = 90
b = 181.705	β = 90
c = 181.705	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary