2QT8 | pdb_00002qt8

Coproporphyrinogen III oxidase from Leishmania major

• PDB DOI: https://doi.org/10.2210/pdb2QT8/pdb

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


• Deposited: 2007-08-01 Released: 2007-09-04 
• Deposition Author(s): Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Coproporphyrinogen III oxidase from Leishmania major.

Merritt, E.A., Le Trong, I.

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: 71.62 kDa 
• Atom Count: 5,545 
• Modeled Residue Count: 606 
• Deposited Residue Count: 618 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrinogen III oxidase	A, B	309	Leishmania major	Mutation(s): 0  Gene Names: LmjF06.1270, LMAJ006828 EC: 1.3.3.3
UniProt
Find proteins for P84155 (Leishmania major) Explore P84155  Go to UniProtKB:  P84155

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.083	α = 86.28
b = 53.808	β = 77.28
c = 65.828	γ = 60.99

Software Package:

Software Name	Purpose
TRUNCATE	data reduction
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-04 
Deposition Author(s): Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2007-09-04
  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
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-16
  Changes: Structure summary