+Open data
-Basic information
Entry | Database: PDB / ID: 1kqw | ||||||
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Title | Crystal structure of holo-CRBP from zebrafish | ||||||
Components | Cellular retinol-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / retinol / vitamin A / retinol-binding | ||||||
Function / homology | Function and homology information Retinoid metabolism and transport / fatty acid transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Calderone, V. / Folli, C. / Marchesani, A. / Berni, R. / Zanotti, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Identification and structural analysis of a zebrafish apo and holo cellular retinol-binding protein. Authors: Calderone, V. / Folli, C. / Marchesani, A. / Berni, R. / Zanotti, G. #1: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallographic Studies on a Family of Cellular Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-binding ...Title: Crystallographic Studies on a Family of Cellular Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-binding Protein in Complex with All-trans-retinol Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystal structures of holo and apo-cellular retinol-binding protein II Authors: Winter, N.S. / Bratt, J.M. / Banaszak, L.J. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Identification, retinoid binding and X-ray analysis of a human retinol-binding protein Authors: Folli, C. / Calderone, V. / Ottonello, S. / Bolchi, A. / Zanotti, G. / Stoppini, M. / Berni, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kqw.cif.gz | 78.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kqw.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 1kqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/1kqw ftp://data.pdbj.org/pub/pdb/validation_reports/kq/1kqw | HTTPS FTP |
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-Related structure data
Related structure data | 1kqxC 1opbS 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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Unit cell |
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-Components
#1: Protein | Mass: 15699.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UVG6 |
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#2: Chemical | ChemComp-RTL / |
#3: 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: 2.1 Å3/Da / Density % sol: 49.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: PEG 4000, Ammonium acetate, sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→40 Å / Num. all: 22343 / Num. obs: 22343 / % possible obs: 72.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.38→1.46 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.9 / Num. unique all: 581 / Rsym value: 0.234 / % possible all: 13.2 |
Reflection | *PLUS Lowest resolution: 21 Å / Num. obs: 22248 / % possible obs: 82.4 % / Num. measured all: 144066 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Lowest resolution: 1.45 Å / % possible obs: 72.3 % / Rmerge(I) obs: 0.234 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OPB Resolution: 1.38→20.989 Å / Num. parameters: 11921 / Num. restraintsaints: 14123 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 4 / Occupancy sum non hydrogen: 1319.21 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.38→20.989 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 22198 / Rfactor all: 0.1654 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.154 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.299 |