2VSW

The structure of the rhodanese domain of the human dual specificity phosphatase 16

• PDB DOI: https://doi.org/10.2210/pdb2VSW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-04-30 Released: 2008-07-15 
• Deposition Author(s): Murray, J.W., Barr, A., Pike, A.C.W., Elkins, J., Phillips, C., Wang, J., Savitsky, P., Roos, A., Bishop, S., Wickstroem, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Burgess-Brown, N., Pantic, N., Bray, J., von Delft, F., Gileadi, O., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.227 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

The Structure of the Rhodanese Domain of the Human Dual Specifity Phosphatase 16

Murray, J.W., Barr, A., Pike, A.C.W., Elkins, J., Phillips, C., Wang, J., Salah, E., Niesen, F., Savitsky, P., Roos, A., Bishop, S., Wickstroem, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Burgess-Brown, N., Pantic, N., Bray, J., von Delft, F., Gileadi, O., Knapp, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2,123 
• Modelled Residue Count: 268 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUAL SPECIFICITY PROTEIN PHOSPHATASE 16	A, B	153	Homo sapiens	Mutation(s): 0  EC: 3.1.3.16 (UniProt), 3.1.3.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY84 (Homo sapiens) Explore Q9BY84  Go to UniProtKB:  Q9BY84
PHAROS:  Q9BY84 GTEx:  ENSG00000111266

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.227 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.451	α = 90
b = 69.128	β = 90
c = 61.017	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Murray, J.W., Barr, A., Pike, A.C.W., Elkins, J., Phillips, C., Wang, J., Savitsky, P., Roos, A., Bishop, S., Wickstroem, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Burgess-Brown, N., Pantic, N., Bray, J., von Delft, F., Gileadi, O., Knapp, S.

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description