7YLS

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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.168 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

Literature

Structure of a bacteria protein complex

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

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

Macromolecules

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 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES (Subject of Investigation/LOI)	D [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], F [auth B], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FE (Subject of Investigation/LOI)	H [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.168 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.613	α = 90
b = 135.613	β = 90
c = 135.613	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Zhang, H., Ma, Y.J., Yu, G.M., Li, X.Z.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2024-04-03
  Changes: Data collection, Refinement description