9WCV | pdb_00009wcv

IscU D40A variant from Methanothrix thermoacetophila

PDB DOI: https://doi.org/10.2210/pdb9WCV/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Methanothrix thermoacetophila PT
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-08-18 Released: 2026-08-26
Deposition Author(s): Kunichika, K., Fujishiro, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.198 (Depositor)

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

Literature

Structural evidence for plasticity of conformations and associations of IscU

Kunichika, K., Fujishiro, T.

To be published.

Macromolecule Content

Total Structure Weight: 60.88 kDa
Atom Count: 3,942
Modeled Residue Count: 493
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen-fixing NifU domain protein	A, B, C, D	137	Methanothrix thermoacetophila PT	Mutation(s): 1 Gene Names: iscU
UniProt
Find proteins for A0B757 (Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT)) Explore A0B757 Go to UniProtKB: A0B757
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0B757
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.49	α = 90
b = 40.28	β = 100.91
c = 90.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	17K14510
Japan Society for the Promotion of Science (JSPS)	Japan	25J01693

Revision History (Full details and data files)

Version 1.0: 2026-08-26
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.