5LKV

Dehaloperoxidase B from Amphitrite ornata: imidazole complex

• PDB DOI: https://doi.org/10.2210/pdb5LKV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amphitrite ornata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-25 Released: 2017-08-16 
• Deposition Author(s): Chicano, T.M., Dworkowski, F.S.N., Hough, M.A.
• Funding Organization(s): Leverhulme Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.141 
• R-Value Work: 0.122 
• R-Value Observed: 0.123 

Starting Model: experimental

Literature

Dehaloperoxidase B from Amphitrite ornata: imidazole complex

Chicano, T.M., Hough, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.77 kDa 
• Atom Count: 2,869 
• Modelled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase B	A, B	137	Amphitrite ornata	Mutation(s): 0
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata) Explore Q9NAV7  Go to UniProtKB:  Q9NAV7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	D [auth A], E [auth A], F [auth A], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	G [auth A], K [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.141 
• R-Value Work: 0.122 
• R-Value Observed: 0.123 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.359	α = 90
b = 67.359	β = 90
c = 67.522	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Chicano, T.M., Dworkowski, F.S.N., Hough, M.A.

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Funding Organization	Location	Grant Number
Leverhulme Trust	United Kingdom	RPG-2014-355

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2018-12-19
  Changes: Author supporting evidence, Data collection, Derived calculations
• Version 1.2: 2024-01-10
  Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description