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Open data
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Basic information
Entry | Database: PDB / ID: 2f33 | ||||||
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Title | NMR solution structure of Ca2+-loaded calbindin D28K | ||||||
![]() | Calbindin | ||||||
![]() | METAL BINDING PROTEIN / ef-hand / Ca2+-binding | ||||||
Function / homology | ![]() metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / cuticular plate / metanephric part of ureteric bud development / retina layer formation / regulation of presynaptic cytosolic calcium ion concentration / response to auditory stimulus / vitamin D metabolic process ...metanephric connecting tubule development / calcium ion binding involved in regulation of presynaptic cytosolic calcium ion concentration / calcium ion binding involved in regulation of postsynaptic cytosolic calcium ion concentration / metanephric distal convoluted tubule development / cuticular plate / metanephric part of ureteric bud development / retina layer formation / regulation of presynaptic cytosolic calcium ion concentration / response to auditory stimulus / vitamin D metabolic process / vitamin D binding / short-term memory / stereocilium / metanephric collecting duct development / presynaptic cytosol / regulation of long-term synaptic potentiation / postsynaptic cytosol / : / cochlea development / calyx of Held / GABA-ergic synapse / long-term memory / hippocampal mossy fiber to CA3 synapse / locomotory behavior / regulation of synaptic plasticity / terminal bouton / retina development in camera-type eye / postsynapse / dendritic spine / learning or memory / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / dendrite / zinc ion binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | SOLUTION NMR / torsion angle dynamics molecular dynamics simulated annealing | ||||||
![]() | Kojetin, D.J. / Venters, R.A. / Kordys, D.R. / Thompson, R.J. / Kumar, R. / Cavanagh, J. | ||||||
![]() | ![]() Title: Structure, binding interface and hydrophobic transitions of Ca(2+)-loaded calbindin-D(28K). Authors: Kojetin, D.J. / Venters, R.A. / Kordys, D.R. / Thompson, R.J. / Kumar, R. / Cavanagh, J. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 812.7 KB | Display | ![]() |
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PDB format | ![]() | 678.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 348.7 KB | Display | ![]() |
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Full document | ![]() | 735.5 KB | Display | |
Data in XML | ![]() | 127.3 KB | Display | |
Data in CIF | ![]() | 175 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 30173.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using a combination of 3D, 4D and (4,2)D projection reconstruction techniques on perdeuterated and fully protonated samples. |
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Sample preparation
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: torsion angle dynamics molecular dynamics simulated annealing Software ordinal: 1 Details: the structures are based on 6882 NOE distance constraints, 432 dihedral angle restraints, 36 hydrogen bond restraints and 304 residual dipolar coupling restraints | ||||||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy Conformers calculated total number: 900 / Conformers submitted total number: 10 |