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), 0.260 (DCC)
R-Value Work:
0.236 (Depositor), 0.240 (DCC)
R-Value Observed:
0.237 (Depositor)

wwPDB Validation 3D Report Full Report

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

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(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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), 0.260 (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

View Full Validation Report

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

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.