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Yorodumi- PDB-2a6y: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6y | ||||||
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Title | Crystal structure of Emp47p carbohydrate recognition domain (CRD), tetragonal crystal form | ||||||
Components | Emp47p (form1) | ||||||
Keywords | SUGAR BINDING PROTEIN / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å | ||||||
Authors | Satoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Kato, R. / Nakano, A. / Wakatsuki, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a6y.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a6y.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 2a6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6y ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6y | HTTPS FTP |
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-Related structure data
Related structure data | 2a6vC 2a6wC 2a6xC 2a6zC 2a70C 2a71C C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28499.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3), DL41 / References: GenBank: 854516, UniProt: P43555*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: Sodium dihydrogen phosphate, Dipotassium hydrogen phosphate, Lithium sulfate, CAPS, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.42→50 Å / Num. all: 48179 / Num. obs: 48001 / % possible obs: 99.6 % / Redundancy: 13.6 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14 | ||||||||||||||||||
Reflection shell | Resolution: 1.42→1.47 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3.6 / Num. unique all: 4735 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.42→10 Å / Num. parameters: 19410 / Num. restraintsaints: 23334 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2141.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→10 Å
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Refine LS restraints |
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