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)

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)

wwPDB Validation 3D Report Full Report

Validation slider image for 4Q9T

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Vanderwaltozyma polyspora Nup133 Beta-propeller domain

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7TDS5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-06-04

Deposition Author(s):

Sampathkumar, P.

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 (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.