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- PDB-6w9o: Crystal structure of an OTU deubiquitinase from Wolbachia pipient... -

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Basic information

Entry
Database: PDB / ID: 6w9o
TitleCrystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel
ComponentsOTU domain-containing protein wMelOTU
KeywordsHYDROLASE / Deubiquitinase / Bacterial effector
Function / homologyOTU domain / OTU domain profile. / ACETATE ION / OTU domain-containing protein
Function and homology information
Biological speciesWolbachia pipientis wMel (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsSchubert, A.F. / Pruneda, J.N. / Komander, D.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192732 United Kingdom
European Research Council (ERC)309456European Union
CitationJournal: Embo J. / Year: 2020
Title: Identification and characterization of diverse OTU deubiquitinases in bacteria.
Authors: Schubert, A.F. / Nguyen, J.V. / Franklin, T.G. / Geurink, P.P. / Roberts, C.G. / Sanderson, D.J. / Miller, L.N. / Ovaa, H. / Hofmann, K. / Pruneda, J.N. / Komander, D.
History
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5472
Polymers24,4881
Non-polymers591
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.543, 56.641, 63.956
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 OTU domain-containing protein wMelOTU


Mass: 24488.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia pipientis wMel (bacteria) / Gene: WD_0443 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HU7
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 32% PEG 4K, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.47→33 Å / Num. obs: 33057 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.061 / Net I/σ(I): 15.4 / Num. measured all: 141445 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.54.10.754661916260.7850.4190.8662.799.9
8.05-333.80.0249252410.9990.0140.02849.398.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSJan 10, 2014data reduction
Aimless0.3.6data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C0R

3c0r


Resolution: 1.47→33 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.48
RfactorNum. reflection% reflection
Rfree0.1898 1677 5.08 %
Rwork0.1632 --
obs0.1646 33002 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.48 Å2 / Biso mean: 27.0821 Å2 / Biso min: 10.45 Å2
Refinement stepCycle: final / Resolution: 1.47→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 4 185 1467
Biso mean--58.14 41.97 -
Num. residues----162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.510.30261280.262625782706100
1.51-1.560.23521610.234525702731100
1.56-1.620.25161350.219125862721100
1.62-1.680.24911250.191925952720100
1.68-1.760.2431430.185725882731100
1.76-1.850.2251370.16752531266899
1.85-1.970.18771400.162626232763100
1.97-2.120.19031560.147925882744100
2.12-2.330.17441370.142526242761100
2.33-2.670.19151180.15372619273798
2.67-3.360.16241500.153226522802100
3.36-330.17521470.1572771291899
Refinement TLS params.Method: refined / Origin x: -5.6051 Å / Origin y: -11.0613 Å / Origin z: 19.9715 Å
111213212223313233
T0.0939 Å2-0.0183 Å20.0013 Å2-0.0898 Å2-0.0028 Å2--0.0868 Å2
L1.8758 °2-0.5864 °20.0775 °2-1.8748 °2-0.4286 °2--1.3356 °2
S-0.0079 Å °-0.0224 Å °0.0354 Å °-0.0524 Å °0.0465 Å °0.0001 Å °-0.0204 Å °-0.0774 Å °-0.0274 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA36 - 210
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allS1 - 209
4X-RAY DIFFRACTION1allB1 - 2

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