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)

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)

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

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

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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	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

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:

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

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Entry History

Deposition Data

Released Date: 2020-11-25

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.