1O12 | pdb_00001o12

Crystal structure of N-acetylglucosamine-6-phosphate deacetylase (TM0814) from Thermotoga maritima at 2.5 A resolution

PDB DOI: https://doi.org/10.2210/pdb1O12/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2002-10-15 Released: 2002-12-18
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.251 (Depositor), 0.190 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Crystal structure of N-acetylglucosamine-6-phosphate deacetylase (TM0814) from Thermotoga maritima at 2.5 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 84.49 kDa
Atom Count: 5,828
Modeled Residue Count: 728
Deposited Residue Count: 752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylglucosamine-6-phosphate deacetylase	A, B	376	Thermotoga maritima	Mutation(s): 9 Gene Names: TM0814 EC: 3.5.1.25
UniProt
Find proteins for Q9WZS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZS1 Go to UniProtKB: Q9WZS1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WZS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.251 (Depositor), 0.190 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data: https://doi.org/10.18430/M31O12

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.07	α = 90
b = 85.07	β = 90
c = 206.01	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
SCALEPACK	data scaling
SnB	phasing
MLPHARE	phasing
CCP4	model building
SOLVE	phasing
CNS	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2002-12-18

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2002-12-18
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2017-10-11
Changes: Data collection
Version 1.5: 2018-07-18
Changes: Data collection, Database references
Version 1.6: 2023-01-25
Changes: Database references, Derived calculations
Version 1.7: 2024-11-06
Changes: Data collection, Structure summary

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.