4ZFT | pdb_00004zft

Catalytic domain of Sst2 F403W mutant bound to ubiquitin

PDB DOI: https://doi.org/10.2210/pdb4ZFT/pdb

Classification: HYDROLASE
Organism(s): Schizosaccharomyces pombe 972h-, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2015-04-21 Released: 2015-10-14
Deposition Author(s): Bueno, A.N.
Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.235 (Depositor), 0.236 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of the catalytic domain of Sst2 mutant F403W bound to ubiquitin at 2.3 Angstroms

Bueno, A.N.

To be published.

Macromolecule Content

Total Structure Weight: 62.59 kDa
Atom Count: 4,161
Modeled Residue Count: 523
Deposited Residue Count: 556
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMSH-like protease sst2	A, C	197	Schizosaccharomyces pombe 972h-	Mutation(s): 1 Gene Names: sst2, SPAC19B12.10 EC: 3.4.19
UniProt
Find proteins for Q9P371 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9P371 Go to UniProtKB: Q9P371
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9P371
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, D	81	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47 GTEx: ENSG00000170315
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CG47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth C], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth C] Focus chain K [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], I [auth B], L [auth C], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.235 (Depositor), 0.236 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.82	α = 90
b = 89.397	β = 90
c = 117.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-10-14

Deposition Author(s):

Bueno, A.N.

Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	1R01RR026273

Revision History (Full details and data files)

Version 1.0: 2015-10-14
Type: Initial release
Version 1.1: 2017-08-23
Changes: Data collection, Derived calculations
Version 1.2: 2017-09-20
Changes: Author supporting evidence
Version 1.3: 2019-12-04
Changes: Author supporting evidence
Version 1.4: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description