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

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Basic information

Entry
Database: PDB / ID: 5hzy
TitleCrystal structure of the legionella pneumophila effector protein RavZ - P6322
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 / MOLECULAR REPLACEMENT / Resolution: 2.548 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
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
Revision 1.2Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Mar 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)52,8051
Polymers52,8051
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18410 Å2
2
A: Uncharacterized protein RavZ

A: Uncharacterized protein RavZ


Theoretical massNumber of molelcules
Total (without water)105,6112
Polymers105,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2830 Å2
ΔGint-16 kcal/mol
Surface area33990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.272, 219.272, 65.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

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Components

#1: Protein Uncharacterized protein RavZ


Mass: 52805.449 Da / Num. of mol.: 1 / Fragment: UNP residues 49-502 / 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 4.33 Å3/Da / Density % sol: 71.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.8M Sodium Acetate trihydrate, 200mM NaCl / PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.548→41.439 Å / Num. obs: 30876 / % possible obs: 100 % / Redundancy: 4.6 % / Net I/σ(I): 47.61

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.548→41.439 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.08
RfactorNum. reflection% reflection
Rfree0.2135 2000 6.48 %
Rwork0.1788 --
obs0.181 30865 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.548→41.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 0 65 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093059
X-RAY DIFFRACTIONf_angle_d1.0984131
X-RAY DIFFRACTIONf_dihedral_angle_d18.7241846
X-RAY DIFFRACTIONf_chiral_restr0.056467
X-RAY DIFFRACTIONf_plane_restr0.006525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5483-2.61210.29141400.22932026X-RAY DIFFRACTION100
2.6121-2.68270.29611390.22171998X-RAY DIFFRACTION100
2.6827-2.76160.28041420.20872057X-RAY DIFFRACTION100
2.7616-2.85070.25711410.20742024X-RAY DIFFRACTION100
2.8507-2.95260.24071400.21332027X-RAY DIFFRACTION100
2.9526-3.07080.24691410.21352025X-RAY DIFFRACTION100
3.0708-3.21050.24721420.22052052X-RAY DIFFRACTION100
3.2105-3.37960.24111410.19832048X-RAY DIFFRACTION100
3.3796-3.59130.21231430.1782058X-RAY DIFFRACTION100
3.5913-3.86840.1931430.15832070X-RAY DIFFRACTION100
3.8684-4.25730.19671430.14822065X-RAY DIFFRACTION100
4.2573-4.87250.15141450.13852091X-RAY DIFFRACTION100
4.8725-6.13570.20991460.17022117X-RAY DIFFRACTION100
6.1357-41.4440.20131540.18432207X-RAY DIFFRACTION98
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)
13.04990.0377-0.01123.006-0.71432.72880.0864-0.1004-0.0138-0.139-0.0389-0.17610.33550.0546-0.02970.45940.2258-0.08350.4237-0.03550.427561.554471.2023-8.6906
23.3731-0.7403-0.29271.68040.21292.6874-0.02910.2674-0.1473-0.0890.09480.04080.3235-0.2017-0.03080.32410.1105-0.01660.4302-0.00670.317251.178678.8664-21.4554
30.8974-0.26330.27321.1355-1.31271.9368-0.07080.0444-0.22740.02940.0562-0.03880.73110.0678-0.09580.76390.2667-0.05480.3289-0.02210.501162.801658.1232.8653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 39 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 257 )
3X-RAY DIFFRACTION3chain 'A' and (resid 258 through 430 )

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