7CNV | pdb_00007cnv

Crystal structure of IscU H106C variant

PDB DOI: https://doi.org/10.2210/pdb7CNV/pdb

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

Deposited: 2020-08-03 Released: 2021-08-04
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: 2.23 Å
R-Value Free:
0.233 (Depositor), 0.230 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

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: 89.33 kDa
Atom Count: 5,983
Modeled Residue Count: 768
Deposited Residue Count: 792
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, E A, B, C, D, E, F	132	Methanothrix thermoacetophila	Mutation(s): 1
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] N [auth C] R [auth D] T [auth E] G [auth A], J [auth B], N [auth C], R [auth D], T [auth E], W [auth F]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B] mmCIF format, chain M [auth B]	M [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain V [auth E] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain K [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A] I [auth A] K [auth B] O [auth C] P [auth C] H [auth A], I [auth A], K [auth B], O [auth C], P [auth C], S [auth D], U [auth E], V [auth E], X [auth F], Y [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain V [auth E] Focus chain X [auth F] Focus chain Y [auth F]