7KQA | pdb_00007kqa

Crystal Structure of Glucosamine-6-phosphate deanimase from Strenotrophomonas maltophilia

• PDB DOI: https://doi.org/10.2210/pdb7KQA/pdb

• Classification: HYDROLASE
• Organism(s): Stenotrophomonas maltophilia
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-14 Released: 2020-11-25 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Crystal Structure of Glucosamine-6-phosphate deanimase from Strenotrophomonas maltophilia

DeBouver, N.D., Delker, S.L., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 74.03 kDa 
• Atom Count: 5,822 
• Modeled Residue Count: 677 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron dicitrate transport regulator FecR	A, B	350	Stenotrophomonas maltophilia	Mutation(s): 0  Gene Names: AR275_15025, BWP19_11460

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m37kqa

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.92	α = 90
b = 90.44	β = 90
c = 126.72	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PARROT	phasing
PHASER	phasing
Coot	model building
PHENIX	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2025-10-22
  Changes: Structure summary