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Yorodumi- PDB-7ztq: Crystal structure of the carotenoid-binding protein domain from s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ztq | ||||||||||||
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Title | Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform | ||||||||||||
Components | Carotenoid-binding protein | ||||||||||||
Keywords | TRANSPORT PROTEIN / carotenoid-binding protein / carotenoid transport / CBP / STARD / START domain / Bombyx mori | ||||||||||||
Function / homology | Function and homology information vesicle tethering to endoplasmic reticulum / endoplasmic reticulum-endosome membrane contact site / cholesterol transport / cholesterol binding / late endosome membrane / lysosomal membrane / endoplasmic reticulum membrane Similarity search - Function | ||||||||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||||||||
Authors | Sluchanko, N.N. / Boyko, K.M. / Varfolomeeva, L.A. / Slonimskiy, Y.B. / Egorkin, N.A. / Maksimov, E.G. / Popov, V.O. | ||||||||||||
Funding support | Russian Federation, Germany, 3items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2022 Title: Silkworm carotenoprotein as an efficient carotenoid extractor, solubilizer and transporter. Authors: Sluchanko, N.N. / Slonimskiy, Y.B. / Egorkin, N.A. / Varfolomeeva, L.A. / Faletrov, Y.V. / Moysenovich, A.M. / Parshina, E.Y. / Friedrich, T. / Maksimov, E.G. / Boyko, K.M. / Popov, V.O. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ztq.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ztq.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 7ztq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ztq_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 7ztq_full_validation.pdf.gz | 439.5 KB | Display | |
Data in XML | 7ztq_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 7ztq_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/7ztq ftp://data.pdbj.org/pub/pdb/validation_reports/zt/7ztq | HTTPS FTP |
-Related structure data
Related structure data | 7ztrC 7ztuC 5i9jS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28530.822 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmCBP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8MYA9 |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.99 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 5% v/v Tacsimate, pH 7.0, 0.1 M HEPES, pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873128 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→47.1 Å / Num. obs: 47986 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 20.7 / Num. measured all: 300922 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5I9J Resolution: 1.45→47.1 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.892 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 89.56 Å2 / Biso mean: 25.92 Å2 / Biso min: 14.58 Å2
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Refinement step | Cycle: final / Resolution: 1.45→47.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.452→1.489 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -18.2866 Å / Origin y: -11.7724 Å / Origin z: -17.507 Å
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