6VDT

Crystal Structure of Dehaloperoxidase B in Complex with cofactor Iron(III) Deuteroporphyrin IX and Substrate 4-nitrophenol

• PDB DOI: https://doi.org/10.2210/pdb6VDT/pdb

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


• Deposited: 2019-12-27 Released: 2020-12-30 
• Deposition Author(s): Ghiladi, R.A., de Serrano, V.S., McGuire, A., Malewschik, T.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.223 
• R-Value Work: 0.167 

Literature

Nonnative Heme Incorporation into Multifunctional Globin Increases Peroxygenase Activity an Order and Magnitude Compared to Native Enzyme

McGuire, A.H., Petit, A.R., Kang, J., Malewschik, T., de Serrano, V., Carey, L.M., Ghiladi, R.A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.52 kDa 
• Atom Count: 2,818 
• 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDE (Subject of Investigation/LOI)	C [auth A], J [auth B]	FE(III) DEUTEROPORPHYRIN IX C30 H28 Fe N4 O4 QQYZTXBVPVYDJC-RWRCOHKGSA-L
NPO (Subject of Investigation/LOI)	E [auth A]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
PEG	F [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.223 
• R-Value Work: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.7	α = 90
b = 67.66	β = 90
c = 67.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Currently 6VDT does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-30 
Deposition Author(s): Ghiladi, R.A., de Serrano, V.S., McGuire, A., Malewschik, T.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2020-12-30
  Type: Initial release
  
• Version 1.1: 2021-06-30
  Changes: Data collection
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description