2YY6

Crystal Structure of the phosphoglycolate phosphatase from Aquifex aeolicus VF5

• PDB DOI: https://doi.org/10.2210/pdb2YY6/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-27 Released: 2007-10-30 
• Deposition Author(s): Tanaka, T., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Crystal Structure of the phosphoglycolate phosphatase from Aquifex aeolicus VF5

Tanaka, T., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.23 kDa 
• Atom Count: 3,485 
• Modelled Residue Count: 416 
• Deposited Residue Count: 426 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoglycolate phosphatase	A, B	213	Aquifex aeolicus VF5	Mutation(s): 0  EC: 3.1.3.18
UniProt
Find proteins for O67359 (Aquifex aeolicus (strain VF5)) Explore O67359  Go to UniProtKB:  O67359

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.236 
• R-Value Observed: 0.236 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.247	α = 90
b = 96.247	β = 90
c = 50.703	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
BSS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Tanaka, T., Kumarevel, T.S., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary