6VMT | pdb_00006vmt

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.273 (Depositor), 0.276 (DCC)
R-Value Work:
0.222 (Depositor), 0.217 (DCC)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4Q874
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.273 (Depositor), 0.276 (DCC)
R-Value Work: 0.222 (Depositor), 0.217 (DCC)

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

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Entry History

Deposition Data

Released Date: 2020-02-26

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.