7C8O

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.223
R-Value Work: 0.194
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0B757
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B]	E [auth A], F [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.223
R-Value Work: 0.194
R-Value Observed: 0.201
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-06-09

Deposition Author(s):

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

Revision History (Full details and data files)

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

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 R01GM133198.