3O7N | pdb_00003o7n

The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase from Amphitrite ornata

• PDB DOI: https://doi.org/10.2210/pdb3O7N/pdb

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


• Deposited: 2010-07-30 Released: 2011-07-13 
• Deposition Author(s): de Serrano, V.S., Davis, M.F., Franzen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

The V59W mutation blocks the distal pocket of the hemoglobin - dehaloperoxidase from Amphitirite ornata

Davis, M.F., de Serrano, V.S., Gracz, H., Vendreix, F.A.P., Somasundram, A., Negrerie, M., 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)

Macromolecule Content 

• Total Structure Weight: 33.14 kDa 
• Atom Count: 3,294 
• 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], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BML	D [auth A], H [auth B]	4-BROMOPHENOL C6 H5 Br O GZFGOTFRPZRKDS-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], I [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:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.925	α = 90
b = 67.305	β = 90
c = 69.253	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-13 
Deposition Author(s): de Serrano, V.S., Davis, M.F., Franzen, S.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description