9G9U | pdb_00009g9u

The structure of XynX, a NIF3 family protein from Geobacillus proteiniphilus T-6

• PDB DOI: https://doi.org/10.2210/pdb9G9U/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Geobacillus proteiniphilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-25 Released: 2025-08-06 
• Deposition Author(s): Hadad, N., Pomyalov, S., Lavid, N., Shoham, Y., Shoham, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

The structure of XynX, a NIF3 family protein from Geobacillus proteiniphilus T-6

Hadad, N., Pomyalov, S., Lavid, N., Shoham, Y., Shoham, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.9 kDa 
• Atom Count: 4,482 
• Modeled Residue Count: 522 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP cyclohydrolase 1 type 2 homolog	A, B	270	Geobacillus proteiniphilus	Mutation(s): 0  Gene Names: LG52_1443

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.586	α = 90
b = 58.301	β = 99.728
c = 99.115	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Hadad, N., Pomyalov, S., Lavid, N., Shoham, Y., Shoham, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release