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Yorodumi- PDB-5f58: Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f58 | ||||||
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Title | Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal after 24 hours of incubation at 1.54 Angstrom Resolution | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / all-trans retinal / retinal light absorbing pigment / wavelength regulation | ||||||
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: 1.54 Å | ||||||
Authors | Nosrati, M. / Nossoni, Z. / Geiger, J.H. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of the Q108K:K40L:T51V:R58F mutant of human Cellular Retinol Binding Protein II in complex with All-trans-Retinal after 24 hours of incubation at 1.54 Angstrom Resolution Authors: Nossoni, Z. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f58.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f58.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 5f58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/5f58 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/5f58 | HTTPS FTP |
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-Related structure data
Related structure data | 5f7gC 4exzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15570.489 Da / Num. of mol.: 2 / Mutation: Q108K, K40L, T51V, R58F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P50120 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30% PEG 4000, 0.1M Ammonium Acetate, 0.1M Sodium Acetate pH = 4.5 PH range: 4-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. all: 136653 / Num. obs: 36188 / % possible obs: 96.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.67 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.17 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EXZ Resolution: 1.54→32.553 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.4 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.517 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.54→32.553 Å
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Refine LS restraints |
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LS refinement shell |
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