7YLT

Structure of a bacteria protein

• PDB DOI: https://doi.org/10.2210/pdb7YLT/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: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structure of a bacteria protein

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 153.5 kDa 
• Atom Count: 11,259 
• Modelled Residue Count: 1,441 
• Deposited Residue Count: 1,444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ABC transporter, substrate-binding protein	A [auth B], B [auth D], C, D [auth A]	361	Variovorax paradoxus	Mutation(s): 0  Gene Names: VAPA_1c15920
UniProt
Find proteins for T1X8R6 (Variovorax paradoxus B4) Explore T1X8R6  Go to UniProtKB:  T1X8R6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.228 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.775	α = 85.6
b = 75.745	β = 89.16
c = 119.706	γ = 89.37

Software Package:

Software Name	Purpose
PHENIX	refinement
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