4WA6 | pdb_00004wa6

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

PDB DOI: https://doi.org/10.2210/pdb4WA6/pdb

Classification: hydrolase/transcription
Organism(s): Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae YJM789
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-08-28 Released: 2015-03-04
Deposition Author(s): Wolberger, C., Yan, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free:
0.244 (Depositor), 0.250 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.186 (Depositor)

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.

Macromolecule Content

Total Structure Weight: 175.48 kDa
Atom Count: 11,129
Modeled Residue Count: 1,364
Deposited Residue Count: 1,534
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 8	A, E [auth D]	476	Saccharomyces cerevisiae S288C	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P50102
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription and mRNA export factor SUS1	B, F	96	Saccharomyces cerevisiae S288C	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6WNK7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SAGA-associated factor 11	C, G	99	Saccharomyces cerevisiae YJM789	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A6ZWK1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SAGA-associated factor 73	D [auth E], H	96	Saccharomyces cerevisiae S288C	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53165
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain V [auth G] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain P [auth E] SDF format, chain O [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain W [auth H] MOL2 format, chain V [auth G] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth E] MOL2 format, chain O [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain W [auth H] mmCIF format, chain V [auth G] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth E] mmCIF format, chain O [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	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		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth C] Focus chain P [auth E] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.244 (Depositor), 0.250 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.076	α = 90
b = 68.004	β = 106.75
c = 137.858	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
Coot	model building
HKL-2000	data scaling
PHENIX	refinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2015-03-04

Deposition Author(s):

Wolberger, C.

Yan, M.

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

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Deposit Data

Help and Resources

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

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

Entity ID: 1

UniProt

Entity Groups

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Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 3

UniProt

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Entity ID: 4

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

4WA6 | pdb_00004wa6