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- PDB-6ryb: Structure of deubiquitinase for PR-ubiquitination 1 -Dup1 -

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Basic information

Entry
Database: PDB / ID: 6ryb
TitleStructure of deubiquitinase for PR-ubiquitination 1 -Dup1
Components(Septation initiation protein) x 3
KeywordsCELL INVASION / Legionella pneumophila / Phosphoribose ubiquitination / deubiquitinase / TOXIN
Function / homologySidE, PDE domain / SidE phosphodiesterase (PDE) domain / Septation initiation protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.315 Å
AuthorsDonghyuk, S. / Ivan, D.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB1177 Germany
German Research FoundationSFB902 Germany
CitationJournal: Mol.Cell / Year: 2020
Title: Regulation of Phosphoribosyl-Linked Serine Ubiquitination by Deubiquitinases DupA and DupB.
Authors: Shin, D. / Mukherjee, R. / Liu, Y. / Gonzalez, A. / Bonn, F. / Liu, Y. / Rogov, V.V. / Heinz, M. / Stolz, A. / Hummer, G. / Dotsch, V. / Luo, Z.Q. / Bhogaraju, S. / Dikic, I.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.2May 27, 2020Group: 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Septation initiation protein
B: Septation initiation protein
C: Septation initiation protein


Theoretical massNumber of molelcules
Total (without water)117,9203
Polymers117,9203
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-8 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.259, 87.259, 612.618
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Septation initiation protein


Mass: 39182.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: D1H98_09620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A6VNK6*PLUS
#2: Protein Septation initiation protein


Mass: 39239.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: D1H98_09620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A6VNK6*PLUS
#3: Protein Septation initiation protein


Mass: 39498.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Gene: D1H98_09620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3A6VNK6*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18 - 20 % PEG3350 / PEG4000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate

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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: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.315→47.59 Å / Num. obs: 62273 / % possible obs: 99.88 % / Redundancy: 21.7 % / Rmerge(I) obs: 0.1252 / Rpim(I) all: 0.02734 / Rrim(I) all: 0.1282 / Net I/σ(I): 19.11
Reflection shellResolution: 2.315→2.398 Å / Rmerge(I) obs: 2.296 / Num. unique obs: 5993 / Rpim(I) all: 0.4877 / Rrim(I) all: 2.348

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.12_2829: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B7P

6b7p


Resolution: 2.315→47.589 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.92
RfactorNum. reflection% reflection
Rfree0.2475 2000 3.22 %
Rwork0.2174 --
obs0.2184 62197 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.315→47.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7492 0 0 167 7659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087681
X-RAY DIFFRACTIONf_angle_d0.93810391
X-RAY DIFFRACTIONf_dihedral_angle_d5.0114554
X-RAY DIFFRACTIONf_chiral_restr0.051101
X-RAY DIFFRACTIONf_plane_restr0.0061348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3147-2.37260.37031370.33674127X-RAY DIFFRACTION99
2.3726-2.43670.39821410.32194231X-RAY DIFFRACTION100
2.4367-2.50840.36361380.29484168X-RAY DIFFRACTION100
2.5084-2.58940.31071400.28684211X-RAY DIFFRACTION100
2.5894-2.68190.31581390.27564192X-RAY DIFFRACTION100
2.6819-2.78930.32391410.26854242X-RAY DIFFRACTION100
2.7893-2.91620.33341420.27474284X-RAY DIFFRACTION100
2.9162-3.06990.34781410.26314211X-RAY DIFFRACTION100
3.0699-3.26220.25961410.2484265X-RAY DIFFRACTION100
3.2622-3.51410.24061440.23374314X-RAY DIFFRACTION100
3.5141-3.86750.25071420.20644315X-RAY DIFFRACTION100
3.8675-4.42680.19241470.18414386X-RAY DIFFRACTION100
4.4268-5.5760.19811470.17914448X-RAY DIFFRACTION100
5.576-47.59860.22171600.18474803X-RAY DIFFRACTION100

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