4P52 | pdb_00004p52

Crystal structure of homoserine kinase from Cytophaga hutchinsonii ATCC 33406, NYSGRC Target 032717.

• PDB DOI: https://doi.org/10.2210/pdb4P52/pdb

• Classification: TRANSFERASE
• Organism(s): Cytophaga hutchinsonii ATCC 33406
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-13 Released: 2014-04-02 
• Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal structure of homoserine kinase from Cytophaga hutchinsonii ATCC 33406, NYSGRC Target 032717.

Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R., Bonanno, J.B., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.4 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 315 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine kinase	A	331	Cytophaga hutchinsonii ATCC 33406	Mutation(s): 0  Gene Names: thrB, CHU_0074 EC: 2.7.1.39

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.209 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.608	α = 90
b = 101.608	β = 90
c = 195.982	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PHENIX	model building
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-02 
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2014-04-02
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Structure summary
• Version 1.2: 2017-09-27
  Changes: Advisory, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary