8ZR8 | pdb_00008zr8

The Crystal Structure of Nudix Hydrolase from Bacillus methanolicus C1

PDB DOI: https://doi.org/10.2210/pdb8ZR8/pdb

Classification: HYDROLASE
Organism(s): Bacillus methanolicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-06-04 Released: 2025-06-04
Deposition Author(s): Chen, C.Y., Huang, C.H.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.269 (Depositor), 0.269 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: in silico
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Literature

The Crystal Structure of Nudix Hydrolase from Bacillus methanolicus C1

Chen, C.Y., Huang, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 65.2 kDa
Atom Count: 4,230
Modeled Residue Count: 512
Deposited Residue Count: 570
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methanol dehydrogenase activator	A, B, C	190	Bacillus methanolicus	Mutation(s): 0 Gene Names: act EC: 3
UniProt
Find proteins for Q8KP10 (Bacillus methanolicus) Explore Q8KP10 Go to UniProtKB: Q8KP10
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8KP10
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.269 (Depositor), 0.269 (DCC)
R-Value Work: 0.225 (Depositor), 0.225 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.993	α = 90
b = 106.657	β = 90
c = 194.911	γ = 90

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: 2025-06-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		2021YFC2100100

Revision History (Full details and data files)

Version 1.0: 2025-06-04
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.