3KD3 | pdb_00003kd3

Crystal structure of a phosphoserine phosphohydrolase-like protein from Francisella tularensis subsp. tularensis SCHU S4

• PDB DOI: https://doi.org/10.2210/pdb3KD3/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Francisella tularensis subsp. tularensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-22 Released: 2009-12-15 
• Deposition Author(s): Nocek, B., Zhou, M., Peterson, S., Anderson, W., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.186 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of a phosphoserine phosphohydrolase-like protein from Francisella tularensis subsp. tularensis SCHUS4

Nocek, B., Zhou, M., Peterson, S., Anderson, W., Joachimiak, A., CSGID

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 50.13 kDa 
• Atom Count: 3,810 
• Modeled Residue Count: 432 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoserine phosphohydrolase-like protein	A, B	219	Francisella tularensis subsp. tularensis	Mutation(s): 0  Gene Names: FTT0568, FTT_0568 EC: 3.1.3.3
UniProt
Find proteins for Q5NH99 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NH99  Go to UniProtKB:  Q5NH99

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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: 1.70 Å
• R-Value Free:  0.186 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33kd3

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.574	α = 90
b = 78.798	β = 90
c = 87.918	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-15 
Deposition Author(s): Nocek, B., Zhou, M., Peterson, S., Anderson, W., Joachimiak, A., CSGID, Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-02-08
  Changes: Database references, Structure summary
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary