3PSN | pdb_00003psn

Crystal structure of mouse VPS29 complexed with Mn2+

• PDB DOI: https://doi.org/10.2210/pdb3PSN/pdb
• Entry: 3PSN supersedes: 3LH7

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-02 Released: 2010-12-15 
• Deposition Author(s): Swarbrick, J., Shaw, D., Chhabra, S., Ghai, R., Valkov, E., Norwood, S., Collins, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.195 (Depositor) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Conformational dynamics and biomolecular interactions of VPS29 studied by NMR and X-ray crystallography

Swarbrick, J., Shaw, D., Chhabra, S., Ghai, R., Valkov, E., Norwood, S., Collins, B.

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.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.58 kDa 
• Atom Count: 2,956 
• Modeled Residue Count: 365 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 29	A, B	192	Mus musculus	Mutation(s): 0  Gene Names: Vps29 EC: 3.1.3.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZ88 (Mus musculus) Explore Q9QZ88  Go to UniProtKB:  Q9QZ88
IMPC:  MGI:1928344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.243 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.195 (Depositor) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.437	α = 90
b = 69.122	β = 105.44
c = 69.024	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Swarbrick, J., Shaw, D., Chhabra, S., Ghai, R., Valkov, E., Norwood, S., Collins, B.
• This entry supersedes: 3LH7

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description