3EVT

Crystal structure of phosphoglycerate dehydrogenase from Lactobacillus plantarum

• PDB DOI: https://doi.org/10.2210/pdb3EVT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactiplantibacillus plantarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-13 Released: 2008-10-21 
• Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Do, J., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.288 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 

Literature

Crystal structure of phosphoglycerate dehydrogenase from Lactobacillus plantarum

Bonanno, J.B., Gilmore, M., Bain, K.T., Do, J., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.28 kDa 
• Atom Count: 2,425 
• Modelled Residue Count: 310 
• Deposited Residue Count: 324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate dehydrogenase	A	324	Lactiplantibacillus plantarum	Mutation(s): 0  Gene Names: lp_2790, serA3 EC: 1.1.1.95 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for F9URQ7 (Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)) Explore F9URQ7  Go to UniProtKB:  F9URQ7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.288 
• R-Value Work: 0.230 
• R-Value Observed: 0.232 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.848	α = 90
b = 75.848	β = 90
c = 107.834	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Do, J., Sampathkumar, P., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references