5VCQ | pdb_00005vcq

A Hyrdrogen Producing Hybrid Streptavidin-Diiron Catalyst

• PDB DOI: https://doi.org/10.2210/pdb5VCQ/pdb

• Classification: Biotin Binding Protein
• Organism(s): Streptomyces avidinii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-31 Released: 2018-04-04 
• Deposition Author(s): Simmons, C.R., Roy, A., Vaughn, M.D., Allen, J.P., Ghirlanda, G.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Enhanced Photocatalytic Hydrogen Production by Hybrid Streptavidin-Diiron Catalysts

Roy, A., Vaughn, M.D., Tomlin, J., Coffman, G.J., Kodis, G., Simmons, C.R., Allen, J.P., Ghirlanda, G.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content 

• Total Structure Weight: 76.6 kDa 
• Atom Count: 4,203 
• Modeled Residue Count: 482 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A, B, C, D	183	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629  Go to UniProtKB:  P22629

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BN7	E [auth A], F [auth B], G [auth C], H [auth D]	2-methylpropyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate C14 H24 N2 O3 S TYWDFVAUHFABAM-GVXVVHGQSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.849	α = 90
b = 56.849	β = 90
c = 239.611	γ = 120

Software Package:

Software Name	Purpose
PHENIX	phasing
HKL-2000	data reduction
HKL-2000	data scaling
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Simmons, C.R., Roy, A., Vaughn, M.D., Allen, J.P., Ghirlanda, G.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0001016

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references