7C8O | pdb_00007c8o

Crystal structure of IscU D40A/H106A variant

• PDB DOI: https://doi.org/10.2210/pdb7C8O/pdb

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


• Deposited: 2020-06-03 Released: 2021-06-09 
• Deposition Author(s): Kunichika, K., Takahashi, Y., Fujishiro, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

[2Fe-2S] clusters-assembled dimeric structures of IscU iron-sulfur scaffold

Kunichika, K., Fujishiro, T., Takahashi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.97 kDa 
• Atom Count: 3,692 
• Modeled Residue Count: 467 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrogen-fixing NifU domain protein	A, B, C, D	137	Methanothrix thermoacetophila	Mutation(s): 2
UniProt
Find proteins for A0B757 (Methanothrix thermoacetophila (strain DSM 6194 / JCM 14653 / NBRC 101360 / PT)) Explore A0B757  Go to UniProtKB:  A0B757

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	E [auth A], F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.678	α = 90
b = 60.376	β = 95.78
c = 64.562	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Kunichika, K., Takahashi, Y., Fujishiro, T.

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

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary