+Open data
-Basic information
Entry | Database: PDB / ID: 3ofg | ||||||
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Title | Structured Domain of Caenorhabditis elegans BMY-1 | ||||||
Components | Boca/mesd chaperone for ywtd beta-propeller-egf protein 1 | ||||||
Keywords | CHAPERONE / molecular chaperone / protein folding / YWTD propeller / LDLR / LRP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.367 Å | ||||||
Authors | Collins, M.N. / Hendrickson, W.A. | ||||||
Citation | Journal: Structure / Year: 2011 Title: Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta-Propeller Domains Authors: Collins, M.N. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ofg.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ofg.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ofg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/3ofg ftp://data.pdbj.org/pub/pdb/validation_reports/of/3ofg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11153.080 Da / Num. of mol.: 2 / Fragment: sequence database residues 84-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: bmy-1, F09E5.17 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IG33 #2: Chemical | ChemComp-CL / #3: 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: 1.83 Å3/Da / Density % sol: 32.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15-18% PEG 3350, 300-500mM LiCl2, 100mM Mes pH 5.5, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 24, 2007 / Details: monochromator + mirror |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→36.37 Å / Num. all: 33460 / Num. obs: 33444 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.367→34.033 Å / Occupancy max: 1 / Occupancy min: 0.18 / SU ML: 0.12 / σ(F): 2.05 / Phase error: 16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.974 Å2 / ksol: 0.422 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.1 Å2 / Biso mean: 14.5199 Å2 / Biso min: 0.75 Å2
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Refinement step | Cycle: LAST / Resolution: 1.367→34.033 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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