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- PDB-5io3: Crystal structure of the legionella pneumophila effector protein ... -

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Basic information

Entry
Database: PDB / ID: 5io3
TitleCrystal structure of the legionella pneumophila effector protein RavZ - I422
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 str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.74 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 8, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Mar 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


Theoretical massNumber of molelcules
Total (without water)56,2951
Polymers56,2951
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18510 Å2
Unit cell
Length a, b, c (Å)222.041, 222.041, 71.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

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Components

#1: Protein Uncharacterized protein RavZ


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.9 Å3/Da / Density % sol: 68.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 2.2M NaCl, 28% PEG 3350, 0.1M Imidazole pH6.5

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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 270 / 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: 2.74→39.25 Å / Num. obs: 23220 / % possible obs: 98 % / Redundancy: 10.6 % / Net I/σ(I): 20.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.74→39.25 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 33.29
RfactorNum. reflection% reflection
Rfree0.2866 2000 8.61 %
Rwork0.2244 --
obs0.2298 23216 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.74→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 0 33 3071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113095
X-RAY DIFFRACTIONf_angle_d1.344181
X-RAY DIFFRACTIONf_dihedral_angle_d19.3531876
X-RAY DIFFRACTIONf_chiral_restr0.064474
X-RAY DIFFRACTIONf_plane_restr0.008532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7404-2.80890.43061230.35741307X-RAY DIFFRACTION86
2.8089-2.88480.38811360.37221442X-RAY DIFFRACTION95
2.8848-2.96970.40421410.34671485X-RAY DIFFRACTION96
2.9697-3.06550.39961380.3341478X-RAY DIFFRACTION98
3.0655-3.17510.33141420.29981507X-RAY DIFFRACTION99
3.1751-3.30210.3661430.30741516X-RAY DIFFRACTION99
3.3021-3.45240.37181430.27991522X-RAY DIFFRACTION99
3.4524-3.63430.31351440.23511525X-RAY DIFFRACTION99
3.6343-3.86180.26331450.20691529X-RAY DIFFRACTION99
3.8618-4.15980.27171440.17981535X-RAY DIFFRACTION99
4.1598-4.5780.25461460.16621551X-RAY DIFFRACTION100
4.578-5.23940.23191480.15571568X-RAY DIFFRACTION100
5.2394-6.59730.29041490.22721580X-RAY DIFFRACTION100
6.5973-42.97750.221580.17191672X-RAY DIFFRACTION100
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)
10.88760.3267-0.33130.69520.61391.1748-0.07780.16490.17510.02620.12790.0416-0.2846-0.0352-0.02370.36860.0455-0.08750.1794-0.01560.20355.3837-34.17362.67
20.6723-0.1419-0.45710.19-0.00910.39850.12710.0811-0.2075-0.16220.1011-0.0589-0.22040.33440.00380.4878-0.1787-0.0880.42490.0550.373867.1002-41.44-7.0306
30.34230.0182-0.07520.4729-0.41360.372-0.05810.01980.25060.14080.03170.1803-0.26680.0618-0.15730.5667-0.1079-0.02720.14760.0430.431363.4416-24.012111.7144
40.53310.05170.16360.3431-0.06930.0722-0.0876-0.02330.22050.16440.0646-0.1358-0.15220.05670.0330.6353-0.210.03060.2345-0.14080.510155.9407-10.904734.7923
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 242 )
3X-RAY DIFFRACTION3chain 'A' and (resid 243 through 358 )
4X-RAY DIFFRACTION4chain 'A' and (resid 359 through 433 )

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