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Yorodumi- PDB-2a71: Crystal structure of Emp47p carbohydrate recognition domain (CRD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a71 | ||||||
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Title | Crystal structure of Emp47p carbohydrate recognition domain (CRD), orthorhombic crystal form | ||||||
Components | Emp47p | ||||||
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: 2.7 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 | 2a71.cif.gz | 180.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a71.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 2a71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/2a71 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/2a71 | HTTPS FTP |
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-Related structure data
Related structure data | 2a6vC 2a6wC 2a6xC 2a6yC 2a6zSC 2a70C 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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Unit cell |
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-Components
#1: Protein | Mass: 24819.447 Da / Num. of mol.: 4 / 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 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG4000, Ammonium acetate, Sodium cacodylate, Calcuim chloride, pH 7.0, 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: 2.7→50 Å / Num. all: 25245 / Num. obs: 22129 / % possible obs: 87.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2242 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A6Z Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.887 / SU B: 14.811 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.432 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.969 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 2.7 Å / Num. reflection Rwork: 1537 / Total num. of bins used: 20 |