5LLZ | pdb_00005llz

Dehaloperoxidase B from Amphitrite ornata: benzotriazole complex

• PDB DOI: https://doi.org/10.2210/pdb5LLZ/pdb

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


• Deposited: 2016-07-28 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: 1.14 Å
• R-Value Free: 
  0.179 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Dehaloperoxidase B from Amphitrite ornata: benzotriazole 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 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.66 kDa 
• Atom Count: 2,845 
• Modeled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
0CT	G [auth B]	1H-benzotriazole C6 H5 N3 QRUDEWIWKLJBPS-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.14 Å
• R-Value Free:  0.179 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.68	α = 90
b = 67.07	β = 90
c = 69.01	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	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, Refinement description