5VTT | pdb_00005vtt

Dehaloperoxidase B Y38F mutant

• PDB DOI: https://doi.org/10.2210/pdb5VTT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amphitrite ornata
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-05-18 Released: 2018-05-23 
• Deposition Author(s): Carey, L.M., Ghiladi, R.A.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Probing the Structure-Function Relationship of a Multifunctional Enzyme using Crystallographic Diffraction Methods

Carey, L.M.

(2017) Thesis 

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: 32.38 kDa 
• Atom Count: 2,493 
• 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): 1
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], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXY	D [auth A], H [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.663	α = 90
b = 67.689	β = 90
c = 67.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Carey, L.M., Ghiladi, R.A.

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

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Database references
• Version 1.2: 2019-11-27
  Changes: Author supporting evidence, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description