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- PDB-8pz3: TssM - A USP-like DUB from B. pseudomallei (193-430) -

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Basic information

Entry
Database: PDB / ID: 8pz3
TitleTssM - A USP-like DUB from B. pseudomallei (193-430)
ComponentsTssM
KeywordsHYDROLASE / Deubiquitinase / papain-fold / USP
Function / homologySbsA, Ig-like domain / Bacterial Ig-like domain / : / Papain-like cysteine peptidase superfamily / TssM
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsUthoff, M. / Hermanns, T. / Hofmann, K. / Baumann, U.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO 3783/3-1 Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
CitationJournal: Life Sci Alliance / Year: 2024
Title: The structural basis for deubiquitination by the fingerless USP-type effector TssM.
Authors: Hermanns, T. / Uthoff, M. / Baumann, U. / Hofmann, K.
History
DepositionJul 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TssM
B: TssM


Theoretical massNumber of molelcules
Total (without water)64,3142
Polymers64,3142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The protein appears as monomer during size exclusion chromatography. Removal of the Ig-like domain in which the b-strand swap occurs has no effect on activity. The protein is possibly ...Evidence: The protein appears as monomer during size exclusion chromatography. Removal of the Ig-like domain in which the b-strand swap occurs has no effect on activity. The protein is possibly attached to the cell surface in vivo and might dimerize under these condition.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-21 kcal/mol
Surface area25330 Å2
Unit cell
Length a, b, c (Å)116.850, 116.850, 111.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein TssM


Mass: 32157.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: tssM / Plasmid: pOPIN-K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: D7SFB8

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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: 3.27 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.15 M ammonium chloride, 22 % w/v PEG 3350 and 4 % Dextran sulfate sodium salt Mr 5,000; 1:2, 1:1, 2:1 protein reservoir drop ration; cryoprotected with reservoir + 25% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2021 / Details: default
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.15→74.88 Å / Num. obs: 15249 / % possible obs: 97.6 % / Redundancy: 4.69 % / Biso Wilson estimate: 58.24 Å2 / CC1/2: 0.985 / Rrim(I) all: 0.25 / Net I/σ(I): 5.75
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 4.76 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 1109 / CC1/2: 0.523 / Rrim(I) all: 1.079 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.18rc4_3812refinement
XDSBUILT=20210323data reduction
XSCALEBUILT=20210323data scaling
PHASER2.8.3phasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→50.6 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2753 1526 10.01 %
Rwork0.2291 --
obs0.2336 15239 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.53 Å2
Refinement stepCycle: LAST / Resolution: 3.15→50.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4443 0 0 0 4443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084559
X-RAY DIFFRACTIONf_angle_d0.9466249
X-RAY DIFFRACTIONf_dihedral_angle_d4.554646
X-RAY DIFFRACTIONf_chiral_restr0.049722
X-RAY DIFFRACTIONf_plane_restr0.007832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.250.36191400.33431227X-RAY DIFFRACTION97
3.25-3.370.38661350.30461245X-RAY DIFFRACTION98
3.37-3.50.33251310.29661242X-RAY DIFFRACTION99
3.5-3.660.34681400.27941238X-RAY DIFFRACTION99
3.66-3.860.3331370.25371228X-RAY DIFFRACTION98
3.86-4.10.23731350.22971229X-RAY DIFFRACTION99
4.1-4.410.2571410.19851257X-RAY DIFFRACTION99
4.41-4.860.23511390.19311236X-RAY DIFFRACTION97
4.86-5.560.22341370.1881259X-RAY DIFFRACTION98
5.56-70.24651430.21781263X-RAY DIFFRACTION97
7-50.60.25161480.19981289X-RAY DIFFRACTION96

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