3E8J | pdb_00003e8j

Coproporphyrinogen III oxidase from Leishmania naiffi

• PDB DOI: https://doi.org/10.2210/pdb3E8J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Leishmania naiffi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-19 Released: 2008-09-02 
• Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.245 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structural investigation of a protozoan coproporphyrinogen III oxidase

Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.52 kDa 
• Atom Count: 5,086 
• Modeled Residue Count: 571 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COPROPORPHYRINOGEN III OXIDASE	A, B	306	Leishmania naiffi	Mutation(s): 0  Gene Names: similar to LbrM06_V2.1260 EC: 1.3.3.3
UniProt
Find proteins for D0VWU6 (Leishmania naiffi) Explore D0VWU6  Go to UniProtKB:  D0VWU6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.245 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.097	α = 90
b = 73.147	β = 90
c = 184.745	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description