1VJU | pdb_00001vju

Coproporphyrinogen III oxidase from Leishmania major

PDB DOI: https://doi.org/10.2210/pdb1VJU/pdb

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

Deposited: 2004-03-29 Released: 2004-04-13
Deposition Author(s): Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.180 (Depositor), 0.210 (DCC)
R-Value Work:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VJU

This is version 1.6 of the entry. See complete history.

Literature

Coproporphyrinogen III oxidase from Leishmania major

Structural Genomics of Pathogenic Protozoa Consortium

To be published.

Macromolecule Content

Total Structure Weight: 71.45 kDa
Atom Count: 5,338
Modeled Residue Count: 586
Deposited Residue Count: 618
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coproporphyrinogen III oxidase	A, B	309	Leishmania major	Mutation(s): 0 EC: 1.3.3.3
UniProt
Find proteins for P84155 (Leishmania major) Explore P84155 Go to UniProtKB: P84155
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84155
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.180 (Depositor), 0.210 (DCC)
R-Value Work: 0.151 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.649	α = 86.456
b = 53.734	β = 77.126
c = 66.627	γ = 61.501

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
SHELXD	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-04-13

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2004-04-13
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2018-01-31
Changes: Database references
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-11-13
Changes: Structure summary

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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.