4Q9T | pdb_00004q9t

Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain

• PDB DOI: https://doi.org/10.2210/pdb4Q9T/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Vanderwaltozyma polyspora DSM 70294
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-05-01 Released: 2014-06-04 
• Deposition Author(s): Sampathkumar, P., Bonanno, J.B., Almo, S.C., Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals), New York SGX Research Center for Structural Genomics (NYSGXRC), New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.268 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain

Sampathkumar, P., Bonanno, J.B., Rout, M.P., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 103.72 kDa 
• Atom Count: 6,097 
• Modeled Residue Count: 766 
• Deposited Residue Count: 918 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin NUP133	A, B	459	Vanderwaltozyma polyspora DSM 70294	Mutation(s): 0  Gene Names: Kpol_1018p77, Nup133
UniProt
Find proteins for A7TDS5 (Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294 / BCRC 21397 / CBS 2163 / NBRC 10782 / NRRL Y-8283 / UCD 57-17)) Explore A7TDS5  Go to UniProtKB:  A7TDS5

Small Molecules

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: 3.00 Å
• R-Value Free:  0.268 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.172	α = 90
b = 133.843	β = 90
c = 136.775	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Sampathkumar, P., Bonanno, J.B., Almo, S.C., Nucleocytoplasmic Transport: a Target for Cellular Control (NPCXstals), New York SGX Research Center for Structural Genomics (NYSGXRC), New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary