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Open data
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Basic information
Entry | Database: PDB / ID: 1kt6 | ||||||
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Title | Crystal structure of bovine holo-RBP at pH 9.0 | ||||||
![]() | plasma retinol-binding protein | ||||||
![]() | TRANSPORT PROTEIN / RBP / retinol binding | ||||||
Function / homology | ![]() retinol transport / retinol transmembrane transporter activity / retinal binding / retinol binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Calderone, V. / Berni, R. / Zanotti, G. | ||||||
![]() | ![]() 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: ![]() Title: Crystallographic Refinement of Human Serum Retinol Binding Protein at 2A Resolution. Authors: Cowan, S.W. / Newcomer, M.E. / Jones, T.A. #2: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.7 KB | Display | ![]() |
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PDB format | ![]() | 70 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kt3C ![]() 1kt4C ![]() 1kt5C ![]() 1kt7C ![]() 1hbpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21095.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-RTL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.82 Å3/Da / Density % sol: 40.17 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 100 mM HEPES, 50 mM NaCl, pH 9.0, 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: ![]() ![]() ![]() |
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: 1.098→22.418 Å / Num. all: 62345 / Num. obs: 62345 / % possible obs: 87.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5808 / Rsym value: 0.228 / % possible all: 70.3 |
Reflection | *PLUS Highest resolution: 1.09 Å / Lowest resolution: 40.82 Å / Num. obs: 65032 / % possible obs: 88.2 % / Redundancy: 3.8 % / Num. measured all: 552856 / Rmerge(I) obs: 0.067 |
Reflection shell | *PLUS % possible obs: 70.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HBP Resolution: 1.1→22.418 Å / Num. parameters: 14538 / Num. restraintsaints: 17752 / 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: 1330 / Occupancy sum non hydrogen: 1615 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→22.418 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: 65032 / Num. reflection Rfree: 3252 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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