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- PDB-8q00: TssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430... -

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Basic information

Entry
Database: PDB / ID: 8q00
TitleTssM-Ub-PA complex - A USP-like DUB from B. pseudomallei (193-430) reacted with Ub-PA
Components
  • Polyubiquitin-B
  • TssM
KeywordsHYDROLASE / Deubiquitinase / papain-fold / USP / Ub-PA
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
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like 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
CITRATE ANION / TssM / Tail fiber
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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 27, 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
Revision 1.2Nov 13, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TssM
B: Polyubiquitin-B
C: TssM
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7919
Polymers81,4324
Non-polymers3595
Water13,043724
1
A: TssM
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9905
Polymers40,7162
Non-polymers2743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-13 kcal/mol
Surface area15990 Å2
MethodPISA
2
C: TssM
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8014
Polymers40,7162
Non-polymers852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-10 kcal/mol
Surface area16430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.750, 103.750, 191.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

21A-858-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#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
#2: Protein Polyubiquitin-B


Mass: 8558.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pTXB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 4 types, 729 molecules

#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 724 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium citrate dibasic and 22 % w/v PEG 3350; 1:2, 1:1, 2:1 protein:reservoir ration; cryoprotected with reservoir + 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 11, 2021 / Details: default
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→103.74 Å / Num. obs: 132701 / % possible obs: 99.9 % / Redundancy: 13.42 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.08 / Net I/σ(I): 18.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.62-1.662.3351.1997020.5162.4251
1.66-1.711.75994300.6681.8271
1.71-1.761.27892230.8141.3281
1.76-1.810.95989240.870.9981
1.81-1.870.67386560.9220.7031
1.87-1.940.50484250.9670.5241
1.94-2.010.37981030.9810.3941
2.01-2.090.27778180.990.2871
2.09-2.180.20974990.9930.2171
2.18-2.290.16271820.9950.1691
2.29-2.410.12968920.9970.1341
2.41-2.560.10364810.9970.1071
2.56-2.740.08161140.9980.0841
2.74-2.960.06657130.9990.0691
2.96-3.240.05252930.9990.0541
3.24-3.620.04347980.9990.0441
3.62-4.180.03742710.9990.0381
4.18-5.120.03536440.9980.0361
5.12-7.240.03528850.9990.0371
7.24-103.740.03916480.9970.0421

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHENIX1.20.1-4487refinement
XSCALEBUILT=20210323data scaling
XDSBUILT=20210323data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→91.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.728 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19822 2000 1.5 %RANDOM
Rwork0.17436 ---
obs0.17473 130701 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.719 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 1.62→91.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 23 724 6451
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126015
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165722
X-RAY DIFFRACTIONr_angle_refined_deg1.761.6648246
X-RAY DIFFRACTIONr_angle_other_deg0.5791.57113218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2675794
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.686550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03910946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2951
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027226
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7892.8713038
X-RAY DIFFRACTIONr_mcbond_other2.7892.8713037
X-RAY DIFFRACTIONr_mcangle_it3.7875.1513803
X-RAY DIFFRACTIONr_mcangle_other3.7875.1513804
X-RAY DIFFRACTIONr_scbond_it4.5363.352977
X-RAY DIFFRACTIONr_scbond_other4.5363.352978
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6125.9034419
X-RAY DIFFRACTIONr_long_range_B_refined8.06234.956800
X-RAY DIFFRACTIONr_long_range_B_other8.01331.646576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 146 -
Rwork0.296 9554 -
obs--99.97 %

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