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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.212 (Depositor), 0.211 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YMY

This is version 1.4 of the entry. See complete history.

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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AF18
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.212 (Depositor), 0.211 (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

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Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

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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.