4P7N

Structure of Escherichia coli PgaB C-terminal domain in complex with glucosamine

• PDB DOI: https://doi.org/10.2210/pdb4P7N/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-03-27 Released: 2014-07-02 
• Deposition Author(s): Little, D.J., Li, G., Ing, C., DiFrancesco, B., Bamford, N.C., Robinson, H., Nitz, M., Pomes, R., Howell, P.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.187 
• R-Value Work: 0.147 
• R-Value Observed: 0.150 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 42.98 kDa 
• Atom Count: 3,384 
• Modelled Residue Count: 364 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase	A	367	Escherichia coli K-12	Mutation(s): 0  Gene Names: pgaB, ycdR, b1023, JW5142 EC: 3.5.1
UniProt
Find proteins for P75906 (Escherichia coli (strain K12)) Explore P75906  Go to UniProtKB:  P75906

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCS	B [auth A], C [auth A], D [auth A]	2-amino-2-deoxy-beta-D-glucopyranose C6 H13 N O5 MSWZFWKMSRAUBD-QZABAPFNSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.187 
• R-Value Work: 0.147 
• R-Value Observed: 0.150 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.967	α = 90
b = 78.833	β = 90
c = 115.96	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Little, D.J., Li, G., Ing, C., DiFrancesco, B., Bamford, N.C., Robinson, H., Nitz, M., Pomes, R., Howell, P.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2014-07-23
  Changes: Database references
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.4: 2017-11-22
  Changes: Refinement description
• Version 1.5: 2020-01-08
  Changes: Author supporting evidence
• Version 1.6: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.7: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary