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Yorodumi- PDB-4iru: Crystal Structure of lepB GAP core in a transition state mimetic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4iru | ||||||
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Title | Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE / Arginine finger / Glutamate finger / P-loop motif / Nucleotide binding / Intrinsic GTPase activity / GTP hydrolysis / GTP hydrolysis activator / GTPase activating protein (GAP) / Protein transport / HYDROLASE-HYDROLASE complex | ||||||
Function / homology | Function and homology information positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / microtubule organizing center ...positive regulation of glycoprotein metabolic process / growth hormone secretion / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / microtubule organizing center / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / G protein activity / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / membrane / cytosol Similarity search - Function | ||||||
Biological species | Legionella pneumophila (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | ||||||
Authors | Mishra, A.K. / Delcampo, C.M. / Collins, R.E. / Roy, C.R. / Lambright, D.G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The Legionella pneumophila GTPase Activating Protein LepB Accelerates Rab1 Deactivation by a Non-canonical Hydrolytic Mechanism. Authors: Mishra, A.K. / Del Campo, C.M. / Collins, R.E. / Roy, C.R. / Lambright, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4iru.cif.gz | 289.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4iru.ent.gz | 243.8 KB | Display | PDB format |
PDBx/mmJSON format | 4iru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4iru_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4iru_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4iru_validation.xml.gz | 55.2 KB | Display | |
Data in CIF | 4iru_validation.cif.gz | 73.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4iru ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4iru | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
-Protein , 2 types, 6 molecules ACEBDF
#1: Protein | Mass: 33916.312 Da / Num. of mol.: 3 / Fragment: LepB GAP domain, catalytic core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lepB, lpg2490 / Plasmid: pET28b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q5ZSM7, small monomeric GTPase #2: Protein | Mass: 21175.166 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1, RAB1A / Plasmid: pET15b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P62820, small monomeric GTPase |
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-Non-polymers , 7 types, 69 molecules
#3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-K / #6: Chemical | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 12% PEG4000, 0.1M Hepes, 0.2M potassium acetate, 0.002M aluminium chloride, 0.02M sodium fluoride, 0.01M 2-mercaptoethanol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791, 0.9639 | |||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2011 / Details: Mirrors | |||||||||
Radiation | Monochromator: Double crystal monochromator with horizontal focusing Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→50 Å / Num. obs: 30171 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Rsym value: 0.54 / Net I/σ(I): 3.8 | |||||||||
Reflection shell | Resolution: 3.2→3.283 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.54 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→43.01 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.852 / SU B: 25.04 / SU ML: 0.433 / Cross valid method: THROUGHOUT / ESU R Free: 0.577 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.798 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→43.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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