8S3G | pdb_00008s3g

Atomic structure of truncated worm GdH

• PDB DOI: https://doi.org/10.2210/pdb8S3G/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Heligmosomoides polygyrus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-20 Released: 2025-03-05 
• Deposition Author(s): Mourao, A., Sattler, M., Geerlof, A.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Atomic structure of truncated worm GdH

Mourao, A., Sattler, M., Geerlof, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 118.42 kDa 
• Atom Count: 7,920 
• Modeled Residue Count: 1,008 
• Deposited Residue Count: 1,074 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B	537	Heligmosomoides polygyrus	Mutation(s): 0  Gene Names: HPBE_LOCUS9300
UniProt
Find proteins for A0A183FP08 (Heligmosomoides polygyrus) Explore A0A183FP08  Go to UniProtKB:  A0A183FP08

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.248 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.245	α = 90
b = 151.245	β = 90
c = 146.043	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Mourao, A., Sattler, M., Geerlof, A.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release