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Yorodumi- PDB-2a6x: Crystal structure of Emp46p carbohydrate recognition domain (CRD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6x | ||||||
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Title | Crystal structure of Emp46p carbohydrate recognition domain (CRD), Y131F mutant | ||||||
Components | Emp46p | ||||||
Keywords | SUGAR BINDING PROTEIN / BETA SANDWICH / CARBOHYDRATE BINDING PROTEIN / CARGO RECEPTOR / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information COPII-coated ER to Golgi transport vesicle / mannose binding / endoplasmic reticulum-Golgi intermediate compartment / endoplasmic reticulum to Golgi vesicle-mediated transport / protein transport / carbohydrate binding / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Satoh, T. / Sato, K. / Kanoh, A. / Yamashita, K. / Kato, R. / Nakano, A. / Wakatsuki, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
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 | 2a6x.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a6x.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 2a6x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6x ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6x | HTTPS FTP |
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-Related structure data
Related structure data | 2a6vSC 2a6wC 2a6yC 2a6zC 2a70C 2a71C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25577.084 Da / Num. of mol.: 2 / Fragment: RESIDUES 6-229 / Mutation: Y131F 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: 6323109, UniProt: Q12396*PLUS #2: Chemical | ChemComp-K / | #3: Chemical | #4: 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: 43.3 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG3350, Potassium fluoride, HEPES, Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2004 |
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: 1.55→50 Å / Num. all: 64255 / Num. obs: 63029 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6196 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A6V Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.825 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / 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: 23.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.55 Å / Num. reflection Rwork: 4335 / Total num. of bins used: 20 |