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Yorodumi- PDB-1kxp: CRYSTAL STRUCTURE OF HUMAN VITAMIN D-BINDING PROTEIN IN COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kxp | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN VITAMIN D-BINDING PROTEIN IN COMPLEX WITH SKELETAL ACTIN | ||||||
Components |
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Keywords | CONTRACTILE PROTEIN/PROTEIN BINDING / DBP / vitamin D-binding protein / Actin Scavenger system / Actin-Binding Protein / CONTRACTILE PROTEIN-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding ...vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / lysosomal lumen / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / blood microparticle / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Otterbein, L.R. / Dominguez, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kxp.cif.gz | 173 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kxp.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 1kxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kxp_validation.pdf.gz | 459.6 KB | Display | wwPDB validaton report |
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Full document | 1kxp_full_validation.pdf.gz | 470.9 KB | Display | |
Data in XML | 1kxp_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 1kxp_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kxp ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kxp | HTTPS FTP |
-Related 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: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MUSCLE / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
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#2: Protein | Mass: 51305.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SERUM / Source: (natural) Homo sapiens (human) / References: UniProt: P02774 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
#5: 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: 3.26 Å3/Da / Density % sol: 62.27 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: Peg 8K 12%, Magnesium Acetate 200mM, Sodium Cacodylate 100 mM, Glycerol 20%, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
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: 2.1→40 Å / Num. all: 67774 / Num. obs: 67458 / % possible obs: 99.8 % / Redundancy: 15.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 11 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 11.2 / Num. unique all: 6596 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 1064049 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / % possible obs: 98.8 % / Redundancy: 11 % / Mean I/σ(I) obs: 9.8 |
-Processing
Software |
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Refinement | Resolution: 2.1→40 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: 2.1→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.18 Å
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å |