8Q21

Crystal structure of Vanadium-dependent haloperoxidase R425S mutant (A. marina)

• PDB DOI: https://doi.org/10.2210/pdb8Q21/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Acaryochloris marina
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-08-01 Released: 2024-08-14 
• Deposition Author(s): Zeides, P., Bellmannn-Sickert, K., Zhang, R., Seel, C.J., Most, V., Schroeder, C.T., Groll, M., Gulder, T.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.233 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Starting Model: experimental

Literature

Unraveling the Molecular Basis of Substrate Specificity and Halogen Activation in Vanadium-Dependent Haloperoxidases

Zeides, P., Bellmannn-Sickert, K., Zhang, R., Seel, C.J., Most, V., Schroeder, C.T., Groll, M., Gulder, T.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 73.16 kDa 
• Atom Count: 4,937 
• Modelled Residue Count: 639 
• Deposited Residue Count: 666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vanadium-dependent bromoperoxidase, putative	A	666	Acaryochloris marina	Mutation(s): 1  Gene Names: AM1_4975
UniProt
Find proteins for B0C4R0 (Acaryochloris marina (strain MBIC 11017)) Explore B0C4R0  Go to UniProtKB:  B0C4R0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	B [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.233 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 306.74	α = 90
b = 306.74	β = 90
c = 306.74	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Zeides, P., Bellmannn-Sickert, K., Zhang, R., Seel, C.J., Most, V., Schroeder, C.T., Groll, M., Gulder, T.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release