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- PDB-7w54: Crystal structure of a bacterial OTU DUB with Ub-PA -

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Basic information

Entry
Database: PDB / ID: 7w54
TitleCrystal structure of a bacterial OTU DUB with Ub-PA
Components
  • Lpg2248
  • Polyubiquitin-B
KeywordsHYDROLASE / DUB
Function / homology
Function and homology information


Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / Ubiquitin B / Dot/Icm T4SS effector
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsZhen, X. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis for the dual catalytic activity of the Legionella pneumophila ovarian tumor (OTU) domain deubiquitinase LotA.
Authors: Luo, J. / Ruan, X. / Huang, Z. / Li, Z. / Ye, L. / Wu, Y. / Zhen, X. / Ouyang, S.
History
DepositionNov 29, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 5, 2023Group: Advisory / Derived calculations / Category: pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lpg2248
B: Lpg2248
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5288
Polymers154,4146
Non-polymers1142
Water59433
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.650, 126.090, 207.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lpg2248


Mass: 60167.527 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2248 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ZTB4
#2: Protein
Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 4
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: J3QS39
#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 299 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Magnesium formate, 15% (w/v) PEG 3350, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→69.03 Å / Num. obs: 56934 / % possible obs: 99.1 % / Redundancy: 13.6 % / Biso Wilson estimate: 69.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Net I/σ(I): 2.3
Reflection shellResolution: 2.64→2.71 Å / Num. unique obs: 3288 / CC1/2: 0.845

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHENIXmodel building
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.64→63.045 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1999 3.52 %RANDOM
Rwork0.2165 ---
obs0.2178 56844 98.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 248.93 Å2 / Biso mean: 77.8104 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.64→63.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10498 0 8 33 10539
Biso mean--20 66.94 -
Num. residues----1325
Refinement TLS params.Method: refined / Origin x: 0.99 Å / Origin y: 28.881 Å / Origin z: 66.614 Å
111213212223313233
T0.3771 Å20.0348 Å20.0025 Å2-0.4186 Å20.0113 Å2--0.3664 Å2
L0.3192 °20.0724 °20.1571 °2-0.8264 °20.1597 °2--0.2107 °2
S-0.018 Å °0.0738 Å °-0.004 Å °0.1611 Å °0.0796 Å °0.0686 Å °0.0756 Å °0.0597 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 520
2X-RAY DIFFRACTION1B2 - 520
3X-RAY DIFFRACTION1C1 - 75
4X-RAY DIFFRACTION1D1 - 73
5X-RAY DIFFRACTION1E1 - 75
6X-RAY DIFFRACTION1F1 - 71
7X-RAY DIFFRACTION1A701 - 707
8X-RAY DIFFRACTION1B601 - 620
9X-RAY DIFFRACTION1C101 - 104
10X-RAY DIFFRACTION1D101
11X-RAY DIFFRACTION1E201
12X-RAY DIFFRACTION1A601
13X-RAY DIFFRACTION1E101

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