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- PDB-2a6z: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2a6z | ||||||
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Title | Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1 | ||||||
![]() | Emp47p (form2) | ||||||
![]() | SUGAR BINDING PROTEIN / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | ![]() RHOC GTPase cycle / carbohydrate derivative binding / fungal-type vacuole membrane / COPII-coated ER to Golgi transport vesicle / D-mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / Golgi membrane / endoplasmic reticulum membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Satoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Kato, R. / Nakano, A. / Wakatsuki, S. | ||||||
![]() | ![]() Title: Structures of the carbohydrate recognition domain of Ca2+-independent cargo receptors Emp46p and Emp47p. Authors: Satoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Yamada, Y. / Igarashi, N. / Kato, R. / Nakano, A. / Wakatsuki, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 113.9 KB | Display | ![]() |
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PDB format | ![]() | 86.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.5 KB | Display | ![]() |
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Full document | ![]() | 419.1 KB | Display | |
Data in XML | ![]() | 13.4 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2a6vC ![]() 2a6wC ![]() 2a6xC ![]() 2a6ySC ![]() 2a70C ![]() 2a71C 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 24819.447 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 36.8 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG3350, Ammonium chloride, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 2004 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9779 Å / Relative weight: 1 |
Reflection | Resolution: 1→50 Å / Num. all: 103133 / Num. obs: 99298 / % possible obs: 96.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1→1.04 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 4.9 / Num. unique all: 9156 / % possible all: 88.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2A6Y Resolution: 1→10 Å / Num. parameters: 18836 / Num. restraintsaints: 22535 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2068.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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