+Open data
-Basic information
Entry | Database: PDB / ID: 2bmd | ||||||
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Title | high resolution structure of GDP-bound human Rab4a | ||||||
Components | RAS-RELATED PROTEIN RAB4A | ||||||
Keywords | PROTEIN TRANSPORT / GTP-BINDING PROTEIN / VESICULAR TRANSPORT / ENDOCYTOSIS / PRENYLATION / TRANSPORT | ||||||
Function / homology | Function and homology information Rab protein signal transduction / postsynaptic recycling endosome / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / antigen processing and presentation / vesicle-mediated transport ...Rab protein signal transduction / postsynaptic recycling endosome / insulin-responsive compartment / RAB geranylgeranylation / MET receptor recycling / TBC/RABGAPs / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / antigen processing and presentation / vesicle-mediated transport / small monomeric GTPase / G protein activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cytoplasmic vesicle membrane / recycling endosome membrane / GDP binding / protein transport / early endosome membrane / vesicle / GTPase activity / GTP binding / perinuclear region of cytoplasm / extracellular exosome Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Scheidig, A.J. / Huber, S.K. | ||||||
Citation | Journal: FEBS Lett. / Year: 2005 Title: High Resolution Crystal Structures of Human Rab4A in its Active and Inactive Conformations. Authors: Huber, S.K. / Scheidig, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bmd.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bmd.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 2bmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bmd ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bmd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20990.775 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE-BINDING DOMAIN, RESIDUES 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET19TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20338, small monomeric GTPase | ||
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#2: Chemical | ChemComp-GDP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 30.68 % Description: PARTIALLY REFINED GPPNHP-BOUND RAB4A STRUCTURE WAS USED FOR MOLECULAR REPLACEMENT, SOLVED BY SAME AUTHORS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30% (W/V) PEG 8000, 200MM AMMONIUM SULPHATE, 100MM SODIUM CACODYLATE PH6.5 HANGING DROP 20 DEGREE CELSIUS |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.0721 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 3, 2003 / Details: MIRROR |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0721 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 15669 / % possible obs: 99.8 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.44 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 7.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→18.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.388 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→18.29 Å
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