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- PDB-1ma9: Crystal structure of the complex of human vitamin D binding prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ma9 | ||||||
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Title | Crystal structure of the complex of human vitamin D binding protein and rabbit muscle actin | ||||||
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![]() | TRANSPORT PROTEIN/CONTRACTILE PROTEIN / protein-protein complex / complex formed in plasma / actin scavenger system / TRANSPORT PROTEIN-CONTRACTILE PROTEIN COMPLEX | ||||||
Function / homology | ![]() 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Verboven, C. / Bogaerts, I. / Waelkens, E. / Rabijns, A. / Van Baelen, H. / Bouillon, R. / De Ranter, C. | ||||||
![]() | ![]() Title: Actin-DBP: the perfect structural fit? Authors: Verboven, C. / Bogaerts, I. / Waelkens, E. / Rabijns, A. / Van Baelen, H. / Bouillon, R. / De Ranter, C. #1: ![]() Title: Purification, crystallization and preliminary X-ray investigation of the complex of the human vitamin D binding protein and rabbit muscle actin Authors: Bogaerts, I. / Verboven, C. / Rabijns, A. / Waelkens, E. / Van Baelen, H. / De Ranter, C. #2: ![]() Title: A structural basis for the unique binding features of the human vitamin D-binding protein Authors: Verboven, C. / Rabijns, A. / De Maeyer, M. / Van Baelen, H. / Bouillon, R. / De Ranter, C. #3: ![]() Title: Atomic structure of the actin:DNase I complex Authors: Kabsch, W. / Mannherz, H.G. / Suck, D. / Pai, E.F. / Holmes, K.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.6 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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: 51291.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) ![]() |
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#2: Protein | Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: muscle / Source: (natural) ![]() ![]() |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG 8000, magnesium acetate, sodium cacodylate, glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
Crystal grow | *PLUS Details: Verboven, C.C., (1995) J. Steroid Biochem. Mol. Biol., 54, 11. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 26, 2000 / Details: premirror, triangular monochromator, bent mirror |
Radiation | Monochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 35664 / Num. obs: 33202 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1633 / Rsym value: 0.25 / % possible all: 93.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 33252 / Num. measured all: 97747 |
Reflection shell | *PLUS % possible obs: 93.9 % / Rmerge(I) obs: 0.25 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1ATN, 1J78 Resolution: 2.4→19.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 818801.14 / Data cutoff high rms absF: 818801.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: simulated annealing, torsion angle dynamics, refinement target : maximum likelihood target using amplitudes
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.3355 Å2 / ksol: 0.336072 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.2532 / Rfactor Rwork: 0.1983 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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