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Yorodumi- PDB-2a6z: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6z | ||||||
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Title | Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1 | ||||||
Components | Emp47p (form2) | ||||||
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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1 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 | 2a6z.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a6z.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 2a6z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6z ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6z | HTTPS FTP |
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-Related structure data
Related structure data | 2a6vC 2a6wC 2a6xC 2a6ySC 2a70C 2a71C C: citing same article (ref.) S: Starting model for refinement |
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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: 24819.447 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-227 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 854516, UniProt: P43555*PLUS |
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#2: 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: 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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.9779 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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