4WA6

Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history. 


Literature

Structure of yeast SAGA DUBm with Sgf73 N59D mutant at 2.36 angstroms resolution

Wolberger, C., Yan, M.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 8A,
E [auth D]		476Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UBP8, YMR223W, YM9959.05
EC: 3.4.19.12
UniProt
Find proteins for P50102 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P50102 
Go to UniProtKB:  P50102
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50102
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription and mRNA export factor SUS1
B, F
96Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SUS1, YBR111W-A
UniProt
Find proteins for Q6WNK7 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q6WNK7 
Go to UniProtKB:  Q6WNK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6WNK7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 11
C, G
99Saccharomyces cerevisiae YJM789Mutation(s): 0 
Gene Names: SGF11, SCY_5678
UniProt
Find proteins for A6ZWK1 (Saccharomyces cerevisiae (strain YJM789))
Explore A6ZWK1 
Go to UniProtKB:  A6ZWK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6ZWK1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SAGA-associated factor 73D [auth E],
H		96Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SGF73, YGL066W
UniProt
Find proteins for P53165 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53165 
Go to UniProtKB:  P53165
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53165
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth C],
P [auth E],
Q [auth D],
R [auth D],
S [auth D],
T [auth D],
U [auth D],
V [auth G],
W [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.076α = 90
b = 68.004β = 106.75
c = 137.858γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Blu-Icedata collection
Cootmodel building
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-095822

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 2.1: 2017-11-22
    Changes: Refinement description
  • Version 2.2: 2019-12-25
    Changes: Author supporting evidence
  • Version 2.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Refinement description