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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.219 (Depositor), 0.221 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

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.

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

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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	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.219 (Depositor), 0.221 (DCC)
R-Value Work: 0.190 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.