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- PDB-4kyi: Crystal structure of the phospholipase VipD from Legionella pneum... -

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Basic information

Entry
Database: PDB / ID: 4kyi
TitleCrystal structure of the phospholipase VipD from Legionella pneumophila in complex with the human GTPase Rab5
Components
  • Ras-related protein Rab-5C
  • VipD
Keywordsprotein binding/transport protein / Phospholipase / protein binding-transport protein complex
Function / homology
Function and homology information


plasma membrane to endosome transport / neutrophil degranulation / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / TBC/RABGAPs / azurophil granule membrane / Golgi Associated Vesicle Biogenesis / regulation of endocytosis / endocytic vesicle / endomembrane system ...plasma membrane to endosome transport / neutrophil degranulation / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / TBC/RABGAPs / azurophil granule membrane / Golgi Associated Vesicle Biogenesis / regulation of endocytosis / endocytic vesicle / endomembrane system / lipid catabolic process / lipid droplet / intracellular protein transport / endocytosis / GDP binding / melanosome / Clathrin-mediated endocytosis / early endosome membrane / early endosome / hydrolase activity / endosome / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / extracellular exosome / plasma membrane
Similarity search - Function
Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / small GTPase Rab1 family profile. / Acyl transferase/acyl hydrolase/lysophospholipase / Small GTPase / Ras family / Small GTP-binding protein domain ...Cytosolic phospholipase A2 catalytic domain / Cytosolic phospholipase A2 catalytic domain / Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / small GTPase Rab1 family profile. / Acyl transferase/acyl hydrolase/lysophospholipase / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-5C / VipD
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.075 Å
AuthorsLucas, M. / Gaspar, A.H. / Pallara, C. / Rojas, A.L. / Fernandez-Recio, J. / Machner, M.P. / Hierro, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5.
Authors: Lucas, M. / Gaspar, A.H. / Pallara, C. / Rojas, A.L. / Fernandez-Recio, J. / Machner, M.P. / Hierro, A.
History
DepositionMay 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Jul 29, 2015Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VipD
B: Ras-related protein Rab-5C
C: VipD
D: Ras-related protein Rab-5C
E: VipD
F: Ras-related protein Rab-5C
G: VipD
H: Ras-related protein Rab-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,91925
Polymers320,0858
Non-polymers2,83517
Water0
1
A: VipD
B: Ras-related protein Rab-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,00010
Polymers80,0212
Non-polymers9798
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: VipD
D: Ras-related protein Rab-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5684
Polymers80,0212
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: VipD
F: Ras-related protein Rab-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7226
Polymers80,0212
Non-polymers7014
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: VipD
H: Ras-related protein Rab-5C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6305
Polymers80,0212
Non-polymers6093
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.275, 97.976, 109.849
Angle α, β, γ (deg.)76.570, 80.710, 78.910
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
VipD


Mass: 61229.688 Da / Num. of mol.: 4 / Fragment: unp Residues 19-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: vipD, lpg2831 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZRP9
#2: Protein
Ras-related protein Rab-5C / L1880 / RAB5L


Mass: 18791.492 Da / Num. of mol.: 4 / Fragment: unp Residues 18-182 / Mutation: Q80L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5C, RABL / Production host: Escherichia coli (E. coli) / References: UniProt: P51148

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Non-polymers , 4 types, 17 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 16% PEG6000, 0.1 M Tris-HCl, 0.2 M LiCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013 / Details: Compound Refractive Lenses
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 3.07→30 Å / Num. obs: 67490 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 81.195 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3.07-3.260.6312.09365571027092.6
3.26-3.480.3323.89359011028598.5
3.48-3.760.1866.8833636955398.4
3.76-4.110.09812.4631702887598.7
4.11-4.580.05719.6127938801998.7
4.58-5.270.04226.2425148708298.8
5.27-6.40.0427.2420999598698.8
6.4-8.860.02344.2916399470098.2
8.860.01472.199541272093.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.075→29.827 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7335 / SU ML: 0.47 / σ(F): 1.93 / Phase error: 33.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2803 3407 5.05 %Random
Rwork0.2329 ---
obs0.2353 67479 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.87 Å2 / Biso mean: 54.2796 Å2 / Biso min: 0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.075→29.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21659 0 174 0 21833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00222162
X-RAY DIFFRACTIONf_angle_d0.63129922
X-RAY DIFFRACTIONf_chiral_restr0.0423406
X-RAY DIFFRACTIONf_plane_restr0.0023830
X-RAY DIFFRACTIONf_dihedral_angle_d13.6018325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0748-3.11870.40571190.38112037215676
3.1187-3.16520.46381380.35442707284598
3.1652-3.21460.3971340.34552697283198
3.2146-3.26720.36161520.33432720287298
3.2672-3.32350.36991420.32072689283199
3.3235-3.38390.35631440.31282715285998
3.3839-3.44880.33171490.30132639278899
3.4488-3.51910.34631500.28732695284598
3.5191-3.59550.37881600.2992672283298
3.5955-3.6790.3651260.28212723284998
3.679-3.77090.34231230.2762739286299
3.7709-3.87260.37721360.25682667280399
3.8726-3.98630.30571410.24212708284999
3.9863-4.11470.28771300.23492757288799
4.1147-4.26130.27591480.22412692284099
4.2613-4.43140.26831540.22172690284499
4.4314-4.63240.26231260.21542706283299
4.6324-4.87560.26551560.2142707286399
4.8756-5.17960.29931490.2172711286099
5.1796-5.57710.26531440.22342687283199
5.5771-6.1340.2731500.23522720287099
6.134-7.01150.28081520.22182686283899
7.0115-8.7960.19731360.17712695283198
8.796-29.8280.17711480.16242613276196

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