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- PDB-7fiu: Crystal structure of the DUB domain of Wolbachia cytoplasmic inco... -

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Basic information

Entry
Database: PDB / ID: 7fiu
TitleCrystal structure of the DUB domain of Wolbachia cytoplasmic incompatibility factor CidB from wMel
ComponentsULP_PROTEASE domain-containing protein
KeywordsTOXIN / Wolbachia / cytoplasmic incompatibility / Deubiquitinase
Function / homologyUbiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / cysteine-type peptidase activity / Papain-like cysteine peptidase superfamily / ULP_PROTEASE domain-containing protein
Function and homology information
Biological speciesWolbachia endosymbiont of Drosophila melanogaster (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84 Å
AuthorsXiao, Y.J. / Wang, W. / Chen, X. / Ji, X.Y. / Yang, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81772204 China
CitationJournal: Nat Commun / Year: 2022
Title: Crystal Structures of Wolbachia CidA and CidB Reveal Determinants of Bacteria-induced Cytoplasmic Incompatibility and Rescue.
Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. ...Authors: Wang, H. / Xiao, Y. / Chen, X. / Zhang, M. / Sun, G. / Wang, F. / Wang, L. / Zhang, H. / Zhang, X. / Yang, X. / Li, W. / Wei, Y. / Yao, D. / Zhang, B. / Li, J. / Cui, W. / Wang, F. / Chen, C. / Shen, W. / Su, D. / Bai, F. / Huang, J. / Ye, S. / Zhang, L. / Ji, X. / Wang, W. / Wang, Z. / Hochstrasser, M. / Yang, H.
History
DepositionAug 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ULP_PROTEASE domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,2591
Polymers33,2591
Non-polymers00
Water1,22568
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)48.110, 60.590, 85.550
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 ULP_PROTEASE domain-containing protein / bacteria factor B


Mass: 33259.301 Da / Num. of mol.: 1 / Fragment: DUB domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia endosymbiont of Drosophila melanogaster (bacteria)
Gene: WD_0632 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HD4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 10mM Nickel (II) Chloride hexahydrate, 100mM TRIS pH 8.5, 20% w/v Polyethylene Glycol Monomethyl Ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.84→49.45 Å / Num. obs: 22187 / % possible obs: 99.4 % / Redundancy: 8.6 % / Biso Wilson estimate: 36.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.029 / Rrim(I) all: 0.086 / Net I/σ(I): 14.3 / Num. measured all: 190236 / Scaling rejects: 144
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
1.84-1.899.11.0631451315900.680.3691.1262.198.6
8.23-49.456.50.05619733020.9960.0220.06126.598.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
AutoSolphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 1.84→49.45 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 1008 4.55 %
Rwork0.2092 21140 -
obs0.2105 22148 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.28 Å2 / Biso mean: 46.7845 Å2 / Biso min: 21.5 Å2
Refinement stepCycle: final / Resolution: 1.84→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2111 0 0 68 2179
Biso mean---49.48 -
Num. residues----270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.940.39691380.31132928306698
1.94-2.060.27931450.24422954309999
2.06-2.220.27991280.23143002313099
2.22-2.440.26831500.20932982313299
2.44-2.790.25311400.213330403180100
2.79-3.520.22071540.207430443198100
3.52-49.450.21961530.19643190334399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5562.72660.79512.2792-0.98952.2819-0.4380.504-0.0708-1.44610.1346-0.3683-0.2382-0.43410.25280.63790.05750.04150.3312-0.08060.2422-29.27016.7983-42.3209
24.07060.95282.4653.47940.35746.93680.116-0.32770.0834-0.2247-0.312-0.0932-0.0835-0.10330.19440.29250.0589-0.02550.2722-0.00250.3-23.424810.8151-26.1959
35.89442.16760.67844.9473-0.63286.1801-0.08920.55060.3914-0.34710.1134-0.3983-0.68860.6077-0.05350.38720.0040.00290.37890.03670.2974-1.822817.3214-17.2586
45.8810.67480.13434.6187-0.64284.64530.01020.3495-0.3456-0.2941-0.1535-0.54480.21420.54250.06080.27250.02840.00650.2698-0.01670.2565-2.29364.7991-13.6391
52.99430.39711.2851.7660.00443.13350.0036-0.0998-0.14480.0809-0.03010.0380.0633-0.08420.03040.27990.02430.01430.1873-0.01230.2215-13.37928.4102-4.9517
64.436-0.1921.3113.915-2.04395.8379-0.05540.19610.24080.1266-0.01630.03820.1445-0.0490.09740.42090.0826-0.01030.2862-0.02280.2909-29.054413.6895-32.0616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 837 through 852 )A837 - 852
2X-RAY DIFFRACTION2chain 'A' and (resid 853 through 891 )A853 - 891
3X-RAY DIFFRACTION3chain 'A' and (resid 892 through 952 )A892 - 952
4X-RAY DIFFRACTION4chain 'A' and (resid 953 through 1015 )A953 - 1015
5X-RAY DIFFRACTION5chain 'A' and (resid 1016 through 1085 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1086 through 1121 )A0

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