+Open data
-Basic information
Entry | Database: PDB / ID: 1kt3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of bovine holo-RBP at pH 2.0 | ||||||
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: 1.4 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kt3.cif.gz | 95 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kt3.ent.gz | 71.7 KB | Display | PDB format |
PDBx/mmJSON format | 1kt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kt3_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1kt3_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 1kt3_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1kt3_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/1kt3 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/1kt3 | HTTPS FTP |
-Related structure data
Related structure data | 1kt4C 1kt5C 1kt6C 1kt7C 1hbpS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21095.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P18902 |
---|---|
#2: Chemical | ChemComp-RTL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 43.23 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.399→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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
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
|