7YLS | pdb_00007yls

Structure of a bacteria protein complex

PDB DOI: https://doi.org/10.2210/pdb7YLS/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Variovorax paradoxus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-26 Released: 2023-06-14
Deposition Author(s): Zhang, H., Ma, Y.J., Yu, G.M., Li, X.Z.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.168 (Depositor), 0.168 (DCC)
R-Value Work:
0.152 (Depositor), 0.154 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a bacteria protein complex

Zhang, H., Ma, Y.J., Yu, G.M., Li, X.Z.

To be published.

Macromolecule Content

Total Structure Weight: 69.11 kDa
Atom Count: 5,279
Modeled Residue Count: 594
Deposited Residue Count: 599
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic-ring-hydroxylating dioxygenase beta subunit	A	162	Variovorax paradoxus	Mutation(s): 0 Gene Names: Vapar_1494
UniProt
Find proteins for C5CSP7 (Variovorax paradoxus (strain S110)) Explore C5CSP7 Go to UniProtKB: C5CSP7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5CSP7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rieske (2Fe-2S) domain protein	B	437	Variovorax paradoxus	Mutation(s): 0 Gene Names: Vapar_1493
UniProt
Find proteins for C5CSP6 (Variovorax paradoxus (strain S110)) Explore C5CSP6 Go to UniProtKB: C5CSP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C5CSP6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FES (Subject of Investigation/LOI) Query on FES Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B]	C [auth A], F [auth B], G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B] Focus chain G [auth B]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]