2NYV

X-ray crystal structure of a phosphoglycolate phosphatase from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2NYV/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-11-21 Released: 2006-12-05 
• Deposition Author(s): Ciatto, C., Min, T., Gorman, J., Burley, S.K., Shapiro, L., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.204 

Literature

X-ray crystal structure of a phosphoglycolate phosphatase from Aquifex aeolicus

Ciatto, C., Min, T., Gorman, J., Burley, S.K., Shapiro, L.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.1 kDa 
• Atom Count: 1,950 
• Modelled Residue Count: 217 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycolate phosphatase	A	222	Aquifex aeolicus	Mutation(s): 1  Gene Names: gph EC: 3.1.3.18
UniProt
Find proteins for O67359 (Aquifex aeolicus (strain VF5)) Explore O67359  Go to UniProtKB:  O67359

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.269 
• R-Value Work: 0.204 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.084	α = 90
b = 121.698	β = 90
c = 74.474	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Ciatto, C., Min, T., Gorman, J., Burley, S.K., Shapiro, L., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references