1YJ8 | pdb_00001yj8

Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb1YJ8/pdb

Classification: OXIDOREDUCTASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-01-13 Released: 2005-02-01
Deposition Author(s): Robien, M.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.256 (Depositor), 0.261 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1YJ8

This is version 1.4 of the entry. See complete history.

Literature

Initial structural analysis of Plasmodium falciparum Glycerol-3-phosphate dehydrogenase

Robien, M.A., Hol, W.G.J., Medical Structural Genomics of Pathogenic Protozoa

To be published.

Macromolecule Content

Total Structure Weight: 126.93 kDa
Atom Count: 8,425
Modeled Residue Count: 1,071
Deposited Residue Count: 1,125
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerol-3-phosphate dehydrogenase	A, B, C	375	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PFL0780w EC: 1.1.1.8
UniProt
Find proteins for Q8I5P5 (Plasmodium falciparum (isolate 3D7)) Explore Q8I5P5 Go to UniProtKB: Q8I5P5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8I5P5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.256 (Depositor), 0.261 (DCC)
R-Value Work: 0.236 (Depositor), 0.240 (DCC)
R-Value Observed: 0.237 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 177.455	α = 90
b = 177.455	β = 90
c = 232.699	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History (Full details and data files)

Version 1.0: 2005-02-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2024-02-14
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.