2O55 | pdb_00002o55

Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria

• PDB DOI: https://doi.org/10.2210/pdb2O55/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Galdieria sulphuraria
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-12-05 Released: 2006-12-19 
• Deposition Author(s): Mccoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

Crystal Structure of a putative glycerophosphodiester phosphodiesterase from Galdieria sulphuraria

Mccoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A.

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: 30.12 kDa 
• Atom Count: 2,069 
• Modeled Residue Count: 254 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative glycerophosphodiester phosphodiesterase	A	258	Galdieria sulphuraria	Mutation(s): 0  Gene Names: c454_101305g29.t1 (MSU_Galdi)

Small Molecules

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

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: 2.81 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.427	α = 90
b = 102.427	β = 90
c = 51.709	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Mccoy, J.G., Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-06
  Changes: Structure summary