3LXY | pdb_00003lxy

Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb3LXY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-25 Released: 2010-03-09 
• Deposition Author(s): Nocek, B., Maltseva, N., Kwon, K., Anderson, W., Joachimiak, A., 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: 
  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92

Nocek, B., Maltseva, N., Kwon, K., Makowska-Grzyska, M., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content 

• Total Structure Weight: 36.07 kDa 
• Atom Count: 2,681 
• Modeled Residue Count: 329 
• Deposited Residue Count: 334 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase	A	334	Yersinia pestis	Mutation(s): 0  Gene Names: pdxA, YPO0493, y3682, YP_3686 EC: 1.1.1.262
UniProt
Find proteins for P58719 (Yersinia pestis) Explore P58719  Go to UniProtKB:  P58719

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33lxy

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.939	α = 90
b = 88.105	β = 90
c = 100.511	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Nocek, B., Maltseva, N., Kwon, K., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-12-14
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2025-10-22
  Changes: Structure summary