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- PDB-6ks5: Crystal structure of Legionella pneumophila deubiquitinase Ceg23 -

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Basic information

Entry
Database: PDB / ID: 6ks5
TitleCrystal structure of Legionella pneumophila deubiquitinase Ceg23
ComponentsType IV secretion protein DotSecretion
KeywordsHYDROLASE / enzyme
Function / homologymembrane => GO:0016020 / Type IV secretion protein Dot / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsQiu, J.Z. / Ouyang, S.Y.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The bacterial deubiquitinase Ceg23 regulates the association of Lys-63-linked polyubiquitin molecules on theLegionellaphagosome.
Authors: Ma, K. / Zhen, X. / Zhou, B. / Gan, N. / Cao, Y. / Fan, C. / Ouyang, S. / Luo, Z.Q. / Qiu, J.
History
DepositionAug 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type IV secretion protein Dot
B: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)81,5972
Polymers81,5972
Non-polymers00
Water0
1
A: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)40,7991
Polymers40,7991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type IV secretion protein Dot


Theoretical massNumber of molelcules
Total (without water)40,7991
Polymers40,7991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.350, 71.610, 142.870
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 Type IV secretion protein Dot / Secretion


Mass: 40798.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_07335 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S6F7D4, UniProt: Q5ZV21*PLUS

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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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% polyethylene glycol 4000, 0.2 M sodium cacodylate (pH 6.0) and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 2.8→64.02 Å / Num. obs: 17475 / % possible obs: 99 % / Redundancy: 12.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.036 / Rsym value: 0.128 / Net I/σ(I): 2
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 1226 / CC1/2: 0.901 / % possible all: 97

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data scaling
SHELXphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.8→40.441 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 33.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.299 901 5.17 %
Rwork0.2735 16517 -
obs0.2748 17418 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.83 Å2 / Biso mean: 86.992 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.8→40.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 0 0 4705
Num. residues----614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.97540.34871440.3566266697
2.9754-3.2050.3351520.343268599
3.205-3.52740.37561600.3409271399
3.5274-4.03740.32171370.2893275599
4.0374-5.08520.32631500.24812793100
5.0852-40.4410.23631580.2473290599
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)
11.92840.27891.57342.2759-1.57092.3918-0.2727-0.7088-0.135-0.1489-0.33270.3982-1.2026-0.94750.14650.87580.14430.13250.9769-0.06380.6264-20.624815.1913-19.2563
23.441-4.35281.48117.84742.55477.84010.27940.10360.0452-0.224-0.0949-0.2040.52330.3122-0.10750.3411-0.00230.02150.5026-0.00440.4355-15.4116-1.7086-43.2829
32.9043.3962-0.04217.1201-2.60373.4936-0.3893-0.09770.60370.04960.22580.3032-1.2386-0.41440.35510.90220.1920.08230.7346-0.0780.5241-20.812820.9455-33.3393
44.71160.768-3.60386.01091.38044.35930.3712-0.57420.0881-1.4208-0.67620.1235-1.58320.57370.42390.9327-0.1304-0.09510.7894-0.01810.5078-7.307619.0962-11.7162
50.5805-0.0160.50188.0649-2.03654.7909-0.13470.33150.60630.1990.05920.6359-0.4770.10940.14520.4425-0.0025-0.1390.67310.08540.7604-30.23319.7935-75.43
63.0913.76272.46253.89672.34032.6207-0.4442-0.06660.04850.63110.27270.2904-0.48990.26390.2430.870.1217-0.05990.5952-0.00390.7628-17.859534.705-54.5757
78.8666-0.0940.9296.0152-1.89289.2406-0.0353-0.4701-0.06670.46670.43470.2825-0.0450.04-0.4080.570.14050.05920.58810.06630.5081-25.0679.7247-60.6853
85.779-0.48514.54775.9073-1.05866.66-0.19571.23670.4382-0.1439-0.3263-0.90740.31370.88850.46950.7096-0.03090.00210.88530.09750.5545-17.890814.8211-84.7218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 113 )A15 - 113
2X-RAY DIFFRACTION2chain 'A' and (resid 114 through 213 )A114 - 213
3X-RAY DIFFRACTION3chain 'A' and (resid 214 through 279 )A214 - 279
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 337 )A280 - 337
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 113 )B11 - 113
6X-RAY DIFFRACTION6chain 'B' and (resid 114 through 231 )B114 - 231
7X-RAY DIFFRACTION7chain 'B' and (resid 232 through 279 )B232 - 279
8X-RAY DIFFRACTION8chain 'B' and (resid 280 through 335 )B280 - 335

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