1VLU | pdb_00001vlu

Crystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution

PDB DOI: https://doi.org/10.2210/pdb1VLU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2004-08-16 Released: 2004-08-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.248 (Depositor), 0.244 (DCC)
R-Value Work:
0.210 (Depositor), 0.208 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1VLU

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

Literature

Crystal structure of Gamma-glutamyl phosphate reductase (yor323c) from Saccharomyces cerevisiae at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 103.29 kDa
Atom Count: 6,039
Modeled Residue Count: 792
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-glutamyl phosphate reductase	A, B	468	Saccharomyces cerevisiae	Mutation(s): 6 Gene Names: PRO2, YOR323C EC: 1.2.1.41
UniProt
Find proteins for P54885 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P54885 Go to UniProtKB: P54885
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

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: 2.29 Å
R-Value Free: 0.248 (Depositor), 0.244 (DCC)
R-Value Work: 0.210 (Depositor), 0.208 (DCC)
R-Value Observed: 0.212 (Depositor)

Diffraction Data:

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.041	α = 90
b = 191.081	β = 90
c = 125.57	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
CCP4	data scaling
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-08-24

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2004-08-24
Type: Initial release
Version 1.1: 2008-04-26
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2024-11-13
Changes: Data collection, Refinement description, 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.