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Open data
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Basic information
Entry | Database: PDB / ID: 1kt3 | ||||||
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Title | Crystal structure of bovine holo-RBP at pH 2.0 | ||||||
![]() | 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 | ![]() | 95 KB | Display | ![]() |
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PDB format | ![]() | 71.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.4 KB | Display | ![]() |
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Full document | ![]() | 440.4 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kt4C ![]() 1kt5C ![]() 1kt6C ![]() 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: 1.94 Å3/Da / Density % sol: 43.23 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2 Details: 50 mM Na citrate, 100 mM NaCl, pH 2.0, 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: 1.399→34.246 Å / Num. all: 32419 / Num. obs: 32419 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 1.4→1.47 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1 / Num. unique all: 1249 / Rsym value: 0.464 / % possible all: 42.7 |
Reflection | *PLUS Highest resolution: 1.39 Å / Lowest resolution: 34.3 Å / Num. measured all: 334447 |
Reflection shell | *PLUS Highest resolution: 1.39 Å / % possible obs: 42.7 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HBP Resolution: 1.4→34.246 Å / Num. parameters: 14484 / Num. restraintsaints: 17663 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1609 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→34.246 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: 26941 / Num. reflection Rfree: 1347 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2435 / Rfactor Rwork: 0.1421 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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