3OK5 | pdb_00003ok5

Structure of the H55D mutant of dehaloperoxidase-hemoglobin A from Amphitriti ornata with 4-Bromophenol inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3OK5/pdb

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


• Deposited: 2010-08-24 Released: 2011-09-07 
• Deposition Author(s): Zhao, J., De Serrano, V.S., Franzen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.297 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Effect of the H55D mutation on the kinetics and structure of dehaloperoxidase-hemoglobin A

Zhao, J., De Serrano, V.S., Franzen, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.11 kDa 
• Atom Count: 2,988 
• Modeled Residue Count: 274 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehaloperoxidase A	A, B	137	Amphitrite ornata	Mutation(s): 1  Gene Names: dhpA
UniProt
Find proteins for Q9NAV8 (Amphitrite ornata) Explore Q9NAV8  Go to UniProtKB:  Q9NAV8

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
BML	D [auth A], G [auth B]	4-BROMOPHENOL C6 H5 Br O GZFGOTFRPZRKDS-UHFFFAOYSA-N
SO4	E [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.297 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.055	α = 90
b = 67.6	β = 90
c = 68.49	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Zhao, J., De Serrano, V.S., Franzen, S.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2011-09-14
  Changes: Derived calculations
• Version 1.2: 2018-01-31
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description