6JTI

Crystal structure of native NagZ from Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb6JTI/pdb

Classification: HYDROLASE
Organism(s): Neisseria gonorrhoeae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-04-11 Released: 2020-05-13
Deposition Author(s): Chen, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.233
R-Value Work: 0.214
R-Value Observed: 0.215

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of native NagZ from Neisseria gonorrhoeae

Chen, Y.

To be published.

Macromolecule Content

Total Structure Weight: 257.44 kDa
Atom Count: 16,208
Modelled Residue Count: 2,049
Deposited Residue Count: 2,382
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hexosaminidase	A, B, C, D, E A, B, C, D, E, F	397	Neisseria gonorrhoeae	Mutation(s): 0 Gene Names: nagZ, NGO0135 EC: 3.2.1.52
UniProt
Find proteins for Q5FA94 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090)) Explore Q5FA94 Go to UniProtKB: Q5FA94
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5FA94
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.233
R-Value Work: 0.214
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.017	α = 90
b = 124.088	β = 90
c = 189.92	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-3000	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.