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Yorodumi- PDB-2a6v: Crystal structure of Emp46p carbohydrate recognition domain (CRD)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a6v | ||||||
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Title | Crystal structure of Emp46p carbohydrate recognition domain (CRD), potassium-bound form | ||||||
Components | Emp46p | ||||||
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 RHOC GTPase cycle / COPII-coated ER to Golgi transport vesicle / D-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 / MAD / Resolution: 1.52 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 | 2a6v.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a6v.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 2a6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a6v_validation.pdf.gz | 447.9 KB | Display | wwPDB validaton report |
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Full document | 2a6v_full_validation.pdf.gz | 451.3 KB | Display | |
Data in XML | 2a6v_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 2a6v_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/2a6v ftp://data.pdbj.org/pub/pdb/validation_reports/a6/2a6v | HTTPS FTP |
-Related structure data
Related structure data | 2a6wC 2a6xC 2a6yC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25593.084 Da / Num. of mol.: 2 / Fragment: RESIDUES 6-229 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: 6323109, UniProt: Q12396*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-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: 43.2 % |
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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 |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.52→50 Å / Num. all: 68062 / Num. obs: 67798 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 13.3 | ||||||||||||||||||
Reflection shell | Resolution: 1.52→1.57 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.6 / Num. unique all: 6716 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.52→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.463 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / 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: 17.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→20 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.52 Å / Num. reflection Rwork: 4722 / Total num. of bins used: 20 |