+Open data
-Basic information
Entry | Database: PDB / ID: 1kt5 | ||||||
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Title | Crystal structure of bovine holo-RBP at pH 4.0 | ||||||
Components | Plasma retinol-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / RBP / retinol binding | ||||||
Function / homology | Function and homology information retinol transport / retinol transmembrane transporter activity / retinal binding / retinol binding / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Calderone, V. / Berni, R. / Zanotti, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: High-resolution Structures of Retinol-binding Protein in Complex with Retinol: pH-induced Protein Structural Changes in the Crystal State Authors: Calderone, V. / Berni, R. / Zanotti, G. #1: Journal: Proteins / Year: 1990 Title: Crystallographic Refinement of Human Serum Retinol Binding Protein at 2A Resolution. Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A. #2: Journal: J.Biol.Chem. / Year: 1993 Title: Crystal Structure of Liganded and Unliganded Forms of Bovine Plasma Retinol-Binding Protein Authors: Zanotti, G. / Berni, R. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kt5.cif.gz | 95.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kt5.ent.gz | 72.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kt5 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kt5 | HTTPS FTP |
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-Related structure data
Related structure data | 1kt3C 1kt4C 1kt6C 1kt7C 1hbpS 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: 20195.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P18902 |
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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: 1.73 Å3/Da / Density % sol: 39.7 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 50 mM Na citrate, 100 mM NaCl, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 / Method: vapor diffusion / Details: used microseeding | |||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: CCD / Date: Feb 10, 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: 1.46→40.82 Å / Num. all: 28174 / Num. obs: 28174 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2328 / Rsym value: 0.261 / % possible all: 71.5 |
Reflection | *PLUS Highest resolution: 1.45 Å / Num. obs: 28216 / Num. measured all: 136920 |
Reflection shell | *PLUS % possible obs: 71.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HBP Resolution: 1.46→40.82 Å / Num. parameters: 15096 / Num. restraintsaints: 18203 / 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: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1677 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→40.82 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 28216 / Num. reflection Rfree: 1411 / Rfactor Rfree: 0.2224 / Rfactor Rwork: 0.1428 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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