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Yorodumi- PDB-7ztu: Crystal structure of the carotenoid-binding protein domain from s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ztu | ||||||||||||
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Title | Crystal structure of the carotenoid-binding protein domain from silkworm Bombyx mori (BmCBP) in the apoform, D162L mutant | ||||||||||||
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: 1.9 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 | 7ztu.cif.gz | 110.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ztu.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ztu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ztu_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 7ztu_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 7ztu_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 7ztu_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zt/7ztu ftp://data.pdbj.org/pub/pdb/validation_reports/zt/7ztu | HTTPS FTP |
-Related structure data
Related structure data | 7ztqSC 7ztrC 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: 28528.893 Da / Num. of mol.: 1 / Mutation: D162L 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop Details: 0.7 M Sodium citrate tribasic dihydrate, 0.1 M BIS- TRIS propane, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→46 Å / Num. obs: 19947 / % possible obs: 97.3 % / Redundancy: 4.5 % / CC1/2: 0.967 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.092 / Rrim(I) all: 0.203 / Net I/σ(I): 8.6 / Num. measured all: 88985 / Scaling rejects: 409 | ||||||||||||||||||||||||||||||
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: 7ZTQ Resolution: 1.9→46 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.408 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1705 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.159 / 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: 99.24 Å2 / Biso mean: 33.411 Å2 / Biso min: 14.79 Å2
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Refinement step | Cycle: final / Resolution: 1.9→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 16.6229 Å / Origin y: -12.7471 Å / Origin z: 17.2867 Å
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