8CUK | pdb_00008cuk

X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast

PDB DOI: https://doi.org/10.2210/pdb8CUK/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-05-17 Released: 2022-05-25
Deposition Author(s): Port, S.A., Baker, R.W., Jeffrey, P.D., Hughson, F.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.174 (Depositor), 0.174 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast

Port, S.A., Baker, R.W., Jeffrey, P.D., Hughson, F.M.

To be published.

Macromolecule Content

Total Structure Weight: 127.07 kDa
Atom Count: 8,288
Modeled Residue Count: 994
Deposited Residue Count: 1,137
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase PEP5	A, B, C	379	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: PEP5, END1, VAM1, VPL9, VPS11, VPT11, YMR231W, YM9959.13 EC: 2.3.2.27
UniProt
Find proteins for P12868 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12868 Go to UniProtKB: P12868
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12868
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.22 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.174 (Depositor), 0.174 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.084	α = 90
b = 113.159	β = 90
c = 129.758	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXCD	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM071574

Revision History (Full details and data files)

Version 1.0: 2022-05-25
Type: Initial release
Version 1.1: 2024-02-14
Changes: Data collection

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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.