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Yorodumi- PDB-8dn1: Q108K:K40L:T51C:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to syn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dn1 | ||||||
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Title | Q108K:K40L:T51C:T53A:R58L:Q38F:Q4F mutant of hCRBPII bound to synthetic fluorophore CM1V at pH 7.2 | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / hCRBPII / cellular retinol binding protein II / covalently bound fluorophore | ||||||
Function / homology | Function and homology information vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å | ||||||
Authors | Bingham, C.R. / Borhan, B. / Geiger, J.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Analyst / Year: 2023 Title: Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins. Authors: Maity, S. / Bingham, C. / Sheng, W. / Ehyaei, N. / Chakraborty, D. / Tahmasebi-Nick, S. / Kimmel, T.E. / Vasileiou, C. / Geiger, J.H. / Borhan, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dn1.cif.gz | 50.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dn1.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 8dn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dn1_validation.pdf.gz | 742.2 KB | Display | wwPDB validaton report |
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Full document | 8dn1_full_validation.pdf.gz | 743.3 KB | Display | |
Data in XML | 8dn1_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 8dn1_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/8dn1 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/8dn1 | HTTPS FTP |
-Related structure data
Related structure data | 8d6hC 8d6lC 8d6nC 8db2C 4qztS 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: 15548.548 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-RH6 / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 25% PEG 4000, ammonium acetate, sodium acetate pH 4.0 - 4.8 PH range: 4.0 - 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→29.59 Å / Num. obs: 28092 / % possible obs: 98.13 % / Redundancy: 11.9 % / Biso Wilson estimate: 14.43 Å2 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Net I/σ(I): 30.8 |
Reflection shell | Resolution: 1.32→1.369 Å / Num. unique obs: 2805 / Rpim(I) all: 0.134 / Rrim(I) all: 0.376 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QZT Resolution: 1.32→29.59 Å / SU ML: 0.1259 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 20.7834 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.32 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→29.59 Å
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Refine LS restraints |
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LS refinement shell |
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