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Open data
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Basic information
Entry | Database: PDB / ID: 1kw2 | ||||||
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Title | CRYSTAL STRUCTURE OF UNCOMPLEXED VITAMIN D-BINDING PROTEIN | ||||||
![]() | Vitamin D-binding protein | ||||||
![]() | TRANSPORT PROTEIN / DBP / vitamin D-binding protein / Actin scavenger system / Actin-binding protein | ||||||
Function / homology | ![]() vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / lysosomal lumen / actin binding / blood microparticle / extracellular space ...vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / lysosomal lumen / actin binding / blood microparticle / extracellular space / extracellular exosome / extracellular region / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Otterbein, L.R. / Dominguez, R. | ||||||
![]() | ![]() Title: Crystal structures of the vitamin D-binding protein and its complex with actin: structural basis of the actin-scavenger system. Authors: Otterbein, L.R. / Cosio, C. / Graceffa, P. / Dominguez, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.8 KB | Display | ![]() |
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PDB format | ![]() | 150.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.7 KB | Display | ![]() |
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Full document | ![]() | 386.2 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1kxpSC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Two molecules are present in the asymetric unit. Molecule A is the best one. |
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Components
#1: Protein | Mass: 51305.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: serum / Source: (natural) ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.8 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 200, 28%, Sodium Acetate, 0.1M, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 9, 2001 / Details: BENT CYLINDRICAL Si-MIRROR (RH coating) |
Radiation | Monochromator: Si (III)DOUBLE CRYSTAL,L=1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→60 Å / Num. all: 67333 / Num. obs: 67333 / % possible obs: 94.9 % / Redundancy: 15.5 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 2.15→2.32 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 10.2 / Num. unique all: 16595 / % possible all: 81.2 |
Reflection | *PLUS Lowest resolution: 60 Å / Num. obs: 67175 / Num. measured all: 1041011 |
Reflection shell | *PLUS % possible obs: 81.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: VITAMIN D-BINDING PROTEIN COMPLEXED WITH ACTIN PDB 1KXP Resolution: 2.15→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→60 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.32 Å
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARM | |||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.251 |