8I37 | pdb_00008i37

Helicobacter pylori G6PDH

PDB DOI: https://doi.org/10.2210/pdb8I37/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Helicobacter pylori SS1
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-01-16 Released: 2024-07-24
Deposition Author(s): Zhou, N., Gao, L.Z.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.254 (Depositor), 0.253 (DCC)
R-Value Work:
0.219 (Depositor), 0.221 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Inorganic polysulfide kills Helicobacter pylori by inactivating G6PDH via cysteine polysulfidation

Ning, Z., Gao, L.Z.

To be published.

Macromolecule Content

Total Structure Weight: 199.39 kDa
Atom Count: 14,155
Modeled Residue Count: 1,712
Deposited Residue Count: 1,712
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-6-phosphate 1-dehydrogenase	A, B, C, D	428	Helicobacter pylori SS1	Mutation(s): 0 Gene Names: zwf EC: 1.1.1.49
UniProt
Find proteins for P56110 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56110 Go to UniProtKB: P56110
Find proteins for Q9ZKB2 (Helicobacter pylori (strain J99 / ATCC 700824)) Explore Q9ZKB2 Go to UniProtKB: Q9ZKB2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	Q9ZKB2 P56110
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.254 (Depositor), 0.253 (DCC)
R-Value Work: 0.219 (Depositor), 0.221 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.871	α = 90
b = 153.871	β = 90
c = 250.535	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release