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Yorodumi- PDB-4kyi: Crystal structure of the phospholipase VipD from Legionella pneum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kyi | ||||||
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Title | Crystal structure of the phospholipase VipD from Legionella pneumophila in complex with the human GTPase Rab5 | ||||||
Components |
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Keywords | protein 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 | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.075 Å | ||||||
Authors | Lucas, M. / Gaspar, A.H. / Pallara, C. / Rojas, A.L. / Fernandez-Recio, J. / Machner, M.P. / Hierro, A. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kyi.cif.gz | 473.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kyi.ent.gz | 403.4 KB | Display | PDB format |
PDBx/mmJSON format | 4kyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kyi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4kyi_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4kyi_validation.xml.gz | 94.7 KB | Display | |
Data in CIF | 4kyi_validation.cif.gz | 123.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/4kyi ftp://data.pdbj.org/pub/pdb/validation_reports/ky/4kyi | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | 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 | 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 / #4: Chemical | #5: Chemical | ChemComp-GNP / #6: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.04 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97625 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013 / Details: Compound Refractive Lenses | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 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
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-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 202.87 Å2 / Biso mean: 54.2796 Å2 / Biso min: 0.01 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.075→29.827 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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