4EB5 | pdb_00004eb5

A. fulgidus IscS-IscU complex structure

PDB DOI: https://doi.org/10.2210/pdb4EB5/pdb

Classification: Transferase/metal binding protein
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-03-23 Released: 2012-05-02
Deposition Author(s): Marinoni, E.N., de Oliveira, J.S., Nicolet, Y., Raulfs, E.C., Amara, P., Dean, D.R., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free:
0.279 (Depositor), 0.268 (DCC)
R-Value Work:
0.208 (Depositor)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

(IscS-IscU)2 complex structures provide insights into Fe2S2 biogenesis and transfer.

Marinoni, E.N., de Oliveira, J.S., Nicolet, Y., Raulfs, E.C., Amara, P., Dean, D.R., Fontecilla-Camps, J.C.

(2012) Angew Chem Int Ed Engl 51: 5439-5442

PubMed: 22511353 Search on PubMed
DOI: https://doi.org/10.1002/anie.201201708
Primary Citation Related Structures:
4EB5, 4EB7

Organizational Affiliation

Metalloproteins Unit, Institut de Biologie Structurale J. P. Ebel, Commissariat à l'Énergie Atomique, Centre National de la Recherche Scientifique, Université Joseph Fourier, Grenoble, France.

Macromolecule Content

Total Structure Weight: 119.03 kDa
Atom Count: 7,697
Modeled Residue Count: 1,032
Deposited Residue Count: 1,070
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable cysteine desulfurase 2	A, B	382	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: iscS2, AF_0564 EC: 2.8.1.7
UniProt
Find proteins for O29689 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29689 Go to UniProtKB: O29689
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29689
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NifU protein (NifU-1)	C, D	153	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0 Gene Names: AF_0185, AF_0565
UniProt
Find proteins for P0DMG2 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore P0DMG2 Go to UniProtKB: P0DMG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DMG2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A]	E [auth A], I [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C]	K [auth C], L [auth D]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain K [auth C] Focus chain L [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.279 (Depositor), 0.268 (DCC)
R-Value Work: 0.208 (Depositor)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.411	α = 90
b = 94.897	β = 90
c = 150.585	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-05-02

Deposition Author(s):

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 2012-05-02
Type: Initial release
Version 1.1: 2013-01-02
Changes: Database references
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations