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- PDB-5cqc: Crystal structure of the legionella pneumophila effector protein RavZ -

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Basic information

Entry
Database: PDB / ID: 5cqc
TitleCrystal structure of the legionella pneumophila effector protein RavZ
Componentsputative RavZ protein
KeywordsHYDROLASE / Ulp-family cysteine protease / autophagy inhibitor / PI3P binding domain / legionella pneumophila effector protein
Function / homology
Function and homology information


host intracellular membrane-bounded organelle / symbiont-mediated suppression of host autophagy / protein delipidation / 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
: / Cysteine protease RavZ
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.985 Å
AuthorsHorenkamp, F.A. / Reinisch, K.M.
CitationJournal: Dev.Cell / Year: 2015
Title: The Legionella Anti-autophagy Effector RavZ Targets the Autophagosome via PI3P- and Curvature-Sensing Motifs.
Authors: Horenkamp, F.A. / Kauffman, K.J. / Kohler, L.J. / Sherwood, R.K. / Krueger, K.P. / Shteyn, V. / Roy, C.R. / Melia, T.J. / Reinisch, K.M.
History
DepositionJul 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative RavZ protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2562
Polymers47,1191
Non-polymers1371
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)221.778, 221.778, 72.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein putative RavZ protein


Mass: 47118.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg1683 / Plasmid: pGex6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5ZUV9
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.73 Å3/Da / Density % sol: 74.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 12% PEG 3350, 0.2 M BaCl2, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2014
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.98→110 Å / Num. all: 18551 / Num. obs: 18194 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.3
Reflection shellResolution: 2.98→3.14 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 0.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.985→68.942 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1818 10 %random selection
Rwork0.2143 ---
obs0.218 18179 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.985→68.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 1 1 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092653
X-RAY DIFFRACTIONf_angle_d1.3293609
X-RAY DIFFRACTIONf_dihedral_angle_d14.432903
X-RAY DIFFRACTIONf_chiral_restr0.052428
X-RAY DIFFRACTIONf_plane_restr0.005460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9849-3.06560.44841080.3916966X-RAY DIFFRACTION77
3.0656-3.15580.42661390.36821249X-RAY DIFFRACTION97
3.1558-3.25770.38571390.3091256X-RAY DIFFRACTION100
3.2577-3.37410.31421420.26411275X-RAY DIFFRACTION100
3.3741-3.50920.30751400.28781259X-RAY DIFFRACTION99
3.5092-3.66890.30241420.21641290X-RAY DIFFRACTION99
3.6689-3.86230.24691400.21981255X-RAY DIFFRACTION99
3.8623-4.10420.29041440.20421291X-RAY DIFFRACTION99
4.1042-4.42110.29311400.18921272X-RAY DIFFRACTION99
4.4211-4.86590.18641450.17031299X-RAY DIFFRACTION99
4.8659-5.56970.19851440.18681291X-RAY DIFFRACTION99
5.5697-7.01620.25391440.24491303X-RAY DIFFRACTION99
7.0162-68.96060.22671510.20151355X-RAY DIFFRACTION96
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)
15.15320.35050.46884.6442.89618.1669-0.29440.04860.3533-0.31920.0667-0.0586-0.5721-0.18210.2860.6985-0.0739-0.0160.4480.08340.6864277.717187.22083.1378
22.521-3.5722-0.99877.4004-1.62364.86280.00180.49520.9204-0.3643-0.0905-0.8412-0.50090.78190.09460.9138-0.17830.03350.7620.0670.8192288.9077180.9791-6.3251
31.1550.2186-0.13951.82262.15085.54780.0697-0.12390.719-0.128-0.02560.113-1.76140.2896-0.11241.512-0.1154-0.05630.5664-0.08361.2897279.7884203.56822.7047
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 256 )
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 429 )

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