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- PDB-8efx: Structure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8efx
TitleStructure of OtDUB DUB Domain disulfide crosslinked with Ubiquitin
Components
  • OtDUB
  • Ubiquitin
KeywordsHYDROLASE/SIGNALING PROTEIN / Complex / Deubiquitinase / HYDROLASE / HYDROLASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / cysteine-type peptidase activity / proteolysis
Similarity search - Function
RickCE-like, catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin-like protease family profile domain-containing protein / Tail fiber
Similarity search - Component
Biological speciesOrientia tsutsugamushi (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNegron Teron, K.N. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM126296-02 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Cocrystallization of ubiquitin-deubiquitinase complexes through disulfide linkage.
Authors: Negron Teron, K.I. / Das, C.
History
DepositionSep 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OtDUB
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)37,7722
Polymers37,7722
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, A ubiquitin mutant was disulfide crosslinked with OtDUB using DTNB to help drive crosslink formation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.399, 83.008, 99.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein OtDUB


Mass: 29149.137 Da / Num. of mol.: 1 / Fragment: Deubiquitylase (DUB) domain, residues 1-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orientia tsutsugamushi (bacteria) / Gene: KATO_02133 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2U3RHU0
#2: Protein Ubiquitin


Mass: 8622.922 Da / Num. of mol.: 1 / Mutation: G76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.16M Magnesium chloride, 0.08M Tris at pH 8.5, 24% PEG 8000 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.84→63.7 Å / Num. obs: 30867 / % possible obs: 99.7 % / Redundancy: 6.56 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.57
Reflection shellResolution: 1.85→1.92 Å / Num. unique obs: 3002 / CC1/2: 0.481

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Processing

Software
NameVersionClassification
PDB_EXTRACTdata extraction
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 6UPS

1ubq

6ups


Resolution: 1.85→63.7 Å / SU ML: 0.2536 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2292 2000 6.52 %
Rwork0.1978 28687 -
obs0.1998 30687 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→63.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 0 161 2705
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00682573
X-RAY DIFFRACTIONf_angle_d0.79173493
X-RAY DIFFRACTIONf_chiral_restr0.0496429
X-RAY DIFFRACTIONf_plane_restr0.0047454
X-RAY DIFFRACTIONf_dihedral_angle_d5.0605346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.37721360.33651927X-RAY DIFFRACTION96
1.89-1.940.3291410.30272039X-RAY DIFFRACTION100
1.94-20.28641400.26611999X-RAY DIFFRACTION99.81
2-2.070.28851420.24872045X-RAY DIFFRACTION99.77
2.07-2.140.26591400.23052003X-RAY DIFFRACTION99.17
2.14-2.230.22131420.212043X-RAY DIFFRACTION99.73
2.23-2.330.25591420.20412026X-RAY DIFFRACTION99.95
2.33-2.450.27321420.20422048X-RAY DIFFRACTION100
2.45-2.60.24081430.20642051X-RAY DIFFRACTION99.95
2.6-2.80.2591420.20772039X-RAY DIFFRACTION99.82
2.8-3.090.22111440.21242065X-RAY DIFFRACTION98.97
3.09-3.530.24341440.19042076X-RAY DIFFRACTION99.82
3.53-4.450.19951480.16562103X-RAY DIFFRACTION99.91
4.46-63.70.19851540.18512223X-RAY DIFFRACTION99.62

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