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Yorodumi- PDB-2wwx: Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase do... -
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-Basic information
Entry | Database: PDB / ID: 2wwx | ||||||
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Title | Crystal structure of the SidM/DrrA(GEF/GDF domain)-Rab1(GTPase domain) complex | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / GOLGI APPARATUS / ER-GOLGI TRANSPORT / ENDOPLASMIC RETICULUM / PRENYLATION / LIPOPROTEIN / NUCLEOTIDE-BINDING | ||||||
Function / homology | Function and homology information : / protein guanylylation / positive regulation of glycoprotein metabolic process / growth hormone secretion / AMPylase activity / protein adenylylation / protein adenylyltransferase / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule ...: / protein guanylylation / positive regulation of glycoprotein metabolic process / growth hormone secretion / AMPylase activity / protein adenylylation / protein adenylyltransferase / melanosome transport / COPII-coated vesicle cargo loading / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / host cell cytoplasmic vesicle / Golgi Cisternae Pericentriolar Stack Reorganization / phosphatidylinositol-4-phosphate binding / protein targeting to membrane / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / regulation of GTPase activity / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / endomembrane system / COPI-mediated anterograde transport / vesicle-mediated transport / substrate adhesion-dependent cell spreading / small monomeric GTPase / guanyl-nucleotide exchange factor activity / positive regulation of interleukin-8 production / intracellular protein transport / host cell cytoplasmic vesicle membrane / G protein activity / autophagy / small GTPase binding / endocytosis / melanosome / cell migration / protein guanylyltransferase activity / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / extracellular exosome / extracellular region / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) LEGIONELLA PNEUMOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å | ||||||
Authors | Suh, H.Y. / Lee, D.W. / Woo, J.S. / Oh, B.H. | ||||||
Citation | Journal: Embo J. / Year: 2010 Title: Structural Insights Into the Dual Nucleotide Exchange and Gdi Displacement Activity of Sidm/Drra Authors: Suh, H.Y. / Lee, D.W. / Lee, K.H. / Ku, B. / Choi, S.J. / Woo, J.S. / Kim, Y.G. / Oh, B.H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wwx.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wwx.ent.gz | 64.8 KB | Display | PDB format |
PDBx/mmJSON format | 2wwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wwx_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
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Full document | 2wwx_full_validation.pdf.gz | 425.9 KB | Display | |
Data in XML | 2wwx_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 2wwx_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/2wwx ftp://data.pdbj.org/pub/pdb/validation_reports/ww/2wwx | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar 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: 19875.605 Da / Num. of mol.: 1 / Fragment: GTPASE DOMAIN, RESIDUES 4-178 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62820 | ||
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#2: Protein | Mass: 24293.809 Da / Num. of mol.: 1 / Fragment: RESIDUES 317-533 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Strain: PHILADELPHIA1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q29ST3, UniProt: Q5ZSQ3*PLUS | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDHas protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.28 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 56689 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 10.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 59.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 13.9 / % possible all: 96.7 |
-Processing
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Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.187 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 13.678 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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