6K6L | pdb_00006k6l

YGL082W-catalytic domain

PDB DOI: https://doi.org/10.2210/pdb6K6L/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-06-03 Released: 2019-07-03
Deposition Author(s): Lu, L.N., Wang, F.
Funding Organization(s): National Science Foundation (China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.241 (Depositor), 0.247 (DCC)
R-Value Work:
0.189 (Depositor), 0.202 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Inactivity of YGL082W in vitro due to impairment of conformational change in the catalytic center loop

Lu, L., Guo, Y., Wang, T., Liang, L., Zhao, S., Wang, F., Liu, L.

(2019) Sci China B Chem

DOI: https://doi.org/10.1007/s11426-019-9623-0

Macromolecule Content

Total Structure Weight: 63.78 kDa
Atom Count: 4,486
Modeled Residue Count: 522
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pseudo deubiquitinase	A, B	283	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: YGL082W
UniProt
Find proteins for P53155 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53155 Go to UniProtKB: P53155
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P53155
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.241 (Depositor), 0.247 (DCC)
R-Value Work: 0.189 (Depositor), 0.202 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.94	α = 90
b = 70.64	β = 102.54
c = 68.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-07-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (China)	China	--

Revision History (Full details and data files)

Version 1.0: 2019-07-03
Type: Initial release
Version 1.1: 2020-01-15
Changes: Database references
Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description

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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.