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- PDB-2dur: Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dur | |||||||||
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Title | Crystal structure of VIP36 exoplasmic/lumenal domain, Ca2+/Man2-bound form | |||||||||
![]() | Vesicular integral-membrane protein VIP36 | |||||||||
![]() | PROTEIN TRANSPORT / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR | |||||||||
Function / homology | ![]() COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-coated ER to Golgi transport vesicle / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of phagocytosis ...COPII-mediated vesicle transport / Cargo concentration in the ER / COPI-coated vesicle / exocytic vesicle / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPII-coated ER to Golgi transport vesicle / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of phagocytosis / heat shock protein binding / protein transport / cytoplasmic vesicle / Golgi membrane / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular space / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Satoh, T. / Cowieson, N.P. / Kato, R. / Wakatsuki, S. | |||||||||
![]() | ![]() Title: Structural basis for recognition of high mannose type glycoproteins by mammalian transport lectin VIP36 Authors: Satoh, T. / Cowieson, N.P. / Hakamata, W. / Ideo, H. / Fukushima, K. / Kurihara, M. / Kato, R. / Yamashita, K. / Wakatsuki, S. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.7 KB | Display | ![]() |
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PDB format | ![]() | 95.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2duoC ![]() 2dupC ![]() 2duqSC ![]() 2e6vC ![]() 2dus C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 28931.318 Da / Num. of mol.: 2 / Fragment: RESIDUES 51-301 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 4 types, 430 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.62 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5% PEG4000, 0.3M MgCl2, 3.4mM mannobiose, 0.1M MES (pH 6.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 80482 / Num. obs: 79197 / % possible obs: 98.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7258 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DUQ Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.789 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.65 Å / Num. reflection Rwork: 4955 / Total num. of bins used: 20 |