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- PDB-5izv: Crystal structure of the legionella pneumophila effector protein ... -

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Basic information

Entry
Database: PDB / ID: 5izv
TitleCrystal structure of the legionella pneumophila effector protein RavZ - F222
ComponentsUncharacterized protein RavZ
KeywordsHYDROLASE / Autophagy / Atg8 / deconjugating enzyme / protease / Atg4B
Function / homology
Function and homology information


host intracellular membrane-bounded organelle / protein delipidation / symbiont-mediated suppression of host autophagy / phosphatidylinositol-3-phosphate binding / cysteine-type peptidase activity / host cell cytoplasmic vesicle membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / proteolysis / extracellular region / membrane
Similarity search - Function
: / RavZ C-terminal PI3P-binding domain / RavZ catalytic domain
Similarity search - Domain/homology
Cysteine protease RavZ
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila strain Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.814 Å
AuthorsKwon, D.H. / Kim, L. / Kim, B.-W. / Hong, S.B. / Song, H.K.
CitationJournal: Autophagy / Year: 2017
Title: The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane
Authors: Kwon, D.H. / Kim, S. / Jung, Y.O. / Roh, K.H. / Kim, L. / Kim, B.-W. / Hong, S.B. / Lee, I.Y. / Song, J.H. / Lee, W.C. / Choi, E.J. / Hwang, K.Y. / Song, H.K.
History
DepositionMar 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Sep 5, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Mar 20, 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

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Assembly

Deposited unit
A: Uncharacterized protein RavZ
B: Uncharacterized protein RavZ


Theoretical massNumber of molelcules
Total (without water)112,5912
Polymers112,5912
Non-polymers00
Water00
1
A: Uncharacterized protein RavZ


Theoretical massNumber of molelcules
Total (without water)56,2951
Polymers56,2951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein RavZ


Theoretical massNumber of molelcules
Total (without water)56,2951
Polymers56,2951
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Uncharacterized protein RavZ

A: Uncharacterized protein RavZ


Theoretical massNumber of molelcules
Total (without water)112,5912
Polymers112,5912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_355-x-3/2,-y+1/2,z1
Buried area3890 Å2
ΔGint-19 kcal/mol
Surface area32260 Å2
MethodPISA
4
B: Uncharacterized protein RavZ

B: Uncharacterized protein RavZ


Theoretical massNumber of molelcules
Total (without water)112,5912
Polymers112,5912
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_454-x-1/2,y,-z-1/21
Buried area3450 Å2
ΔGint-19 kcal/mol
Surface area31390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.251, 313.003, 314.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Uncharacterized protein RavZ


Mass: 56295.258 Da / Num. of mol.: 2 / Mutation: C258S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila strain Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg1683 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZUV9

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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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M NaCl, 20% PEG 3350, 0.1M MgCl2, 0.1M Imidazole pH 6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.814→43.55 Å / Num. obs: 42566 / % possible obs: 98 % / Redundancy: 5 % / Net I/σ(I): 36.92

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.814→43.55 Å / Cross valid method: FREE R-VALUE / σ(F): 2.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 2014 4.73 %
Rwork0.1875 --
obs0.1885 42566 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.814→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5873 0 0 0 5873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115981
X-RAY DIFFRACTIONf_angle_d1.4868077
X-RAY DIFFRACTIONf_dihedral_angle_d20.5553623
X-RAY DIFFRACTIONf_chiral_restr0.076917
X-RAY DIFFRACTIONf_plane_restr0.0091026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8141-2.88440.34251340.30592638X-RAY DIFFRACTION90
2.8844-2.96240.33361350.27982801X-RAY DIFFRACTION97
2.9624-3.04950.30241460.27132857X-RAY DIFFRACTION98
3.0495-3.1480.31091410.23922899X-RAY DIFFRACTION98
3.148-3.26040.32921460.23072852X-RAY DIFFRACTION98
3.2604-3.3910.27431390.21462894X-RAY DIFFRACTION99
3.391-3.54520.28191460.19662913X-RAY DIFFRACTION99
3.5452-3.73210.22081460.17342935X-RAY DIFFRACTION99
3.7321-3.96580.19251410.16672942X-RAY DIFFRACTION100
3.9658-4.27180.22421500.1572958X-RAY DIFFRACTION100
4.2718-4.70130.17711460.1432943X-RAY DIFFRACTION100
4.7013-5.38080.19211450.15472981X-RAY DIFFRACTION100
5.3808-6.77590.25381490.20853015X-RAY DIFFRACTION100
6.7759-46.90880.19981500.18662912X-RAY DIFFRACTION93
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)
13.46191.62860.55341.74420.83472.02980.04650.3282-0.4144-0.01030.00650.07560.24380.21610.00090.52140.0294-0.04910.5545-0.14830.4854-38.832362.9821-14.9941
21.2884-0.2711-0.13342.0413-0.06550.99670.08231.06050.641-0.5853-0.2458-0.3925-0.29640.2350.00830.49990.01310.04570.95460.00810.567-30.516877.4015-20.0416
30.83830.17830.39421.68250.22431.59330.19880.64-0.6287-0.1795-0.0979-0.04870.31870.0726-0.56380.5934-0.0214-0.05580.7499-0.33650.5105-54.256156.5412-27.5709
41.99470.62651.17332.36720.75340.8944-0.1014-0.20060.33590.1555-0.00270.1672-0.3053-0.0913-0.00050.5896-0.02330.00740.5852-0.16770.57-31.243417.2202-62.2762
52.05280.0924-0.82771.0054-0.01681.53640.06930.08690.06590.12150.05090.3120.1074-0.4074-0.00010.4548-0.0208-0.00220.4978-0.0570.6523-41.044315.9785-73.3065
61.09280.12510.40711.00110.03121.69220.2055-0.66380.91350.2196-0.14990.0736-0.17460.03480.05190.6712-0.0796-0.05740.5745-0.38380.8753-14.155628.6175-54.2032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 231 )
3X-RAY DIFFRACTION3chain 'A' and (resid 232 through 430 )
4X-RAY DIFFRACTION4chain 'B' and (resid 49 through 136 )
5X-RAY DIFFRACTION5chain 'B' and (resid 137 through 257 )
6X-RAY DIFFRACTION6chain 'B' and (resid 258 through 430 )

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