1YMY | pdb_00001ymy

Crystal Structure of the N-Acetylglucosamine-6-phosphate deacetylase from Escherichia coli K12

• PDB DOI: https://doi.org/10.2210/pdb1YMY/pdb

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


• Deposited: 2005-01-21 Released: 2005-02-01 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Crystal structure of the N-acetylglucosamine-6-phosphate deacetylase from Escherichia Coli

Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C.

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.

Macromolecule Content 

• Total Structure Weight: 81.98 kDa 
• Atom Count: 5,306 
• Modeled Residue Count: 707 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylglucosamine-6-phosphate deacetylase	A, B	382	Escherichia coli K-12	Mutation(s): 0  Gene Names: nagA EC: 3.5.1.25
UniProt
Find proteins for P0AF18 (Escherichia coli (strain K12)) Explore P0AF18  Go to UniProtKB:  P0AF18

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.226	α = 90
b = 114.023	β = 90
c = 80.215	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Xiang, D.F., Raushel, F.M., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references