+Open data
-Basic information
Entry | Database: PDB / ID: 3nkv | ||||||
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Title | Crystal structure of Rab1b covalently modified with AMP at Y77 | ||||||
Components | Ras-related protein Rab-1B | ||||||
Keywords | PROTEIN TRANSPORT / posttranslational modification / AMPylation / adenylylation / Rab1b / vesicular transport | ||||||
Function / homology | Function and homology information positive regulation of glycoprotein metabolic process / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / Golgi organization ...positive regulation of glycoprotein metabolic process / regulation of autophagosome assembly / phagophore assembly site membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / small monomeric GTPase / G protein activity / intracellular protein transport / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å | ||||||
Authors | Mueller, M.P. / Peters, H. / Blankenfeldt, W. / Goody, R.S. / Itzen, A. | ||||||
Citation | Journal: Science / Year: 2010 Title: The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b. Authors: Muller, M.P. / Peters, H. / Blumer, J. / Blankenfeldt, W. / Goody, R.S. / Itzen, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nkv.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nkv.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 3nkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkv ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkv | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19752.369 Da / Num. of mol.: 2 / Fragment: Rab1b-AMP Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1B, RAB1B_HUMAN / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9H0U4 |
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-Non-polymers , 5 types, 253 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 15% (v/v) isopropanol, 15% (w/v) PEG4000, 0.1 M imidazole, 10 mM BaCl2, pH 6.0, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 |
Detector | Type: PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010 / Details: SI(111) |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.8 Å / Num. obs: 33392 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.7→1.8 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.7→19.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.83 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.283 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→19.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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