6XMY | pdb_00006xmy

Crystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella pneumophila in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb6XMY/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-07-01 Released: 2020-07-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Legionella pneumophila in complex with NAD

DeBouver, N.D., Mayclin, S.J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.1 kDa 
• Atom Count: 3,021 
• Modeled Residue Count: 325 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase	A	332	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: pdxA, lpg0299 EC: 1.1.1.262
UniProt
Find proteins for Q3V872 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q3V872  Go to UniProtKB:  Q3V872

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	B [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4	C [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	K [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.35	α = 90
b = 36.77	β = 103.07
c = 56.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-07-22
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2025-10-22
  Changes: Structure summary