3P3D | pdb_00003p3d

Crystal structure of the Nup53 RRM domain from Pichia guilliermondii

• PDB DOI: https://doi.org/10.2210/pdb3P3D/pdb

• Classification: NUCLEAR PROTEIN
• Organism(s): Meyerozyma guilliermondii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-04 Released: 2011-01-19 
• Deposition Author(s): Sampathkumar, P., Shawn, C., Bain, K., Gilmore, J., Gheyi, T., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.288 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Nup53 RRM domain from Pichia guilliermondii

Sampathkumar, P.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.52 kDa 
• Atom Count: 688 
• Modeled Residue Count: 87 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoporin 53	A	132	Meyerozyma guilliermondii	Mutation(s): 0  Gene Names: NUP53 (gi146415668), PGUG_04532
UniProt
Find proteins for A5DMN1 (Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324)) Explore A5DMN1  Go to UniProtKB:  A5DMN1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.288 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.507	α = 90
b = 62.507	β = 90
c = 55.117	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Sampathkumar, P., Shawn, C., Bain, K., Gilmore, J., Gheyi, T., Atwell, S., Thompson, D.A., Emtage, J.S., Wasserman, S., Sauder, J.M., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description