6VMT

Leishmania major Programmed Cell Death Protein 5 Homolog

• PDB DOI: https://doi.org/10.2210/pdb6VMT/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-01-28 Released: 2020-02-26 
• Deposition Author(s): Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 

Starting Model: experimental

Literature

Leishmania major Programmed Cell Death Protein 5 Homolog

Merritt, E.A., Anderson, L., Arakaki, T., Hol, W.G., Le Trong, I., Mehlin, C., Soltis, M., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 13.3 kDa 
• Atom Count: 799 
• Modelled Residue Count: 99 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed Cell Death Protein 5 Homolog	A	117	Leishmania major	Mutation(s): 0  Gene Names: LMJF_28_1920
UniProt
Find proteins for Q4Q874 (Leishmania major) Explore Q4Q874  Go to UniProtKB:  Q4Q874

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.273 
• R-Value Work: 0.222 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.386	α = 90
b = 115.386	β = 90
c = 58.628	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MoRDa	phasing

Structure Validation

Currently 6VMT does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description