[English] 日本語
Yorodumi- PDB-3ofe: Structured Domain of Drosophila melanogaster Boca p41 2 2 Crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ofe | ||||||
---|---|---|---|---|---|---|---|
Title | Structured Domain of Drosophila melanogaster Boca p41 2 2 Crystal form | ||||||
Components | LDLR chaperone boca | ||||||
Keywords | CHAPERONE / mesd / molecular chaperone / protein folding / YWTD propeller / LRP | ||||||
Function / homology | Function and homology information protein targeting to membrane / endomembrane system / endoplasmic reticulum to Golgi vesicle-mediated transport / Wnt signaling pathway / protein folding / apical part of cell / endoplasmic reticulum lumen / endoplasmic reticulum / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.288 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ofe.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ofe.ent.gz | 34.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ofe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ofe_validation.pdf.gz | 419 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ofe_full_validation.pdf.gz | 419.5 KB | Display | |
Data in XML | 3ofe_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 3ofe_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/3ofe ftp://data.pdbj.org/pub/pdb/validation_reports/of/3ofe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 10724.560 Da / Num. of mol.: 2 / Fragment: sequence database residues 88-172 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: boca, CG30498 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8T9B6 #2: Water | ChemComp-HOH / | Has protein modification | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.7 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 18-21% PEG 3350, 100-200mM Na citrate, 100mM CHES pH9.0, and 10mM DTT with macroseeding, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 14.6 % / Av σ(I) over netI: 27.96 / Number: 155098 / Rmerge(I) obs: 0.067 / Χ2: 1 / D res high: 2.5 Å / D res low: 20 Å / Num. obs: 10635 / % possible obs: 85.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→20 Å / Num. all: 15868 / Num. obs: 15757 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.069 / Χ2: 1 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: MAD | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Phasing set |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set |
| |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm | FOM : 0.78 / FOM acentric: 0.79 / FOM centric: 0.76 / Reflection: 5109 / Reflection acentric: 3414 / Reflection centric: 1695 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.288→19.781 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.25 / σ(F): 0.08 / Phase error: 19.45 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.335 Å2 / ksol: 0.359 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 130.75 Å2 / Biso mean: 27.323 Å2 / Biso min: 9.81 Å2
| ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.288→19.781 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
|