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- PDB-5ms8: Crystal structure of the legionella pneumophila effector protein ... -

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Basic information

Entry
Database: PDB / ID: 5ms8
TitleCrystal structure of the legionella pneumophila effector protein RavZ_1-487
ComponentsLegionella pneumophila effector protein RavZ
KeywordsHYDROLASE / Hydrolase / Autophagy / Legionella pneumophila effector protein / ATG8 deconjugating enzyme
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
: / DI(HYDROXYETHYL)ETHER / Cysteine protease RavZ
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila ATCC 33215 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsPantoom, S. / Vetter, I.R. / Wu, Y.W.
CitationJournal: Elife / Year: 2017
Title: Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins.
Authors: Yang, A. / Pantoom, S. / Wu, Y.W.
History
DepositionDec 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Legionella pneumophila effector protein RavZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2544
Polymers54,8731
Non-polymers3813
Water34219
1
A: Legionella pneumophila effector protein RavZ
hetero molecules

A: Legionella pneumophila effector protein RavZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5088
Polymers109,7472
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455y-1/2,x+1/2,-z+1/21
Buried area4370 Å2
ΔGint-29 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.270, 221.270, 73.270
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-619-

HOH

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Components

#1: Protein Legionella pneumophila effector protein RavZ


Mass: 54873.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila ATCC 33215 (bacteria)
Gene: lpg1683 / Plasmid: pOPIN / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5ZUV9
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 16% PEG3350, 0.2 M BaCl2 and 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2015
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.85→47.05 Å / Num. obs: 21565 / % possible obs: 100 % / Redundancy: 26.7 % / Biso Wilson estimate: 86.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.2162 / Net I/σ(I): 14.09
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 27.9 % / Rmerge(I) obs: 1.927 / Mean I/σ(I) obs: 1.85 / CC1/2: 0.134 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CQC

5cqc


Resolution: 2.85→47.047 Å / SU ML: 0.55 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 30.04
RfactorNum. reflection% reflection
Rfree0.2495 1079 5 %
Rwork0.2012 --
obs0.2036 21565 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.85→47.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2967 0 9 19 2995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093027
X-RAY DIFFRACTIONf_angle_d1.4524086
X-RAY DIFFRACTIONf_dihedral_angle_d17.9941122
X-RAY DIFFRACTIONf_chiral_restr0.055465
X-RAY DIFFRACTIONf_plane_restr0.006518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.97970.41141330.38412512X-RAY DIFFRACTION100
2.9797-3.13680.3631320.33652518X-RAY DIFFRACTION100
3.1368-3.33330.34781330.27742532X-RAY DIFFRACTION100
3.3333-3.59050.31221330.222521X-RAY DIFFRACTION100
3.5905-3.95170.20151340.16422541X-RAY DIFFRACTION100
3.9517-4.52310.18321340.15412557X-RAY DIFFRACTION100
4.5231-5.69710.20871370.17232588X-RAY DIFFRACTION100
5.6971-47.05320.26081430.1952717X-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)
15.05060.5007-0.17055.44791.18735.4578-0.22050.0620.2472-0.63230.30220.1735-0.7653-0.2433-0.05810.801-0.0109-0.06160.44480.05260.580154.808187.33833.179
23.4927-2.1906-1.90787.0423-1.51763.72750.02170.3058-0.1182-0.3565-0.0553-0.3545-0.12490.51190.05170.7832-0.11380.00560.61940.03460.563667.5361181.4234-6.0591
30.89680.168-0.27072.94622.89396.4677-0.12450.06180.7131-0.14530.03210.4437-1.68710.33930.03881.2266-0.1595-0.02130.5772-0.07751.03858.4926203.547222.6596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 167 )
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 433 )

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