4GZG

Crystal structures of DHPA-CO complex

• PDB DOI: https://doi.org/10.2210/pdb4GZG/pdb

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


• Deposited: 2012-09-06 Released: 2013-09-11 
• Deposition Author(s): Zhao, J., Franzen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.209 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Starting Model: experimental

Literature

The role of distal histidine in carbonmonoxide DHP structure

Zhao, J., Franzen, S.

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.

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 32.77 kDa 
• Atom Count: 2,891 
• Modelled 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): 0  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], E [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
SO4	F [auth B], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CMO	D [auth A], J [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.209 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.725	α = 90
b = 67.27	β = 90
c = 69.055	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: 2013-09-11 
Deposition Author(s): Zhao, J., Franzen, S.

Revision History  

• Version 1.0: 2013-09-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description