+Open data
-Basic information
Entry | Database: PDB / ID: 6fie | ||||||
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Title | Crystallographic structure of calcium loaded Calbindin-D28K. | ||||||
Components | Calbindin | ||||||
Keywords | METAL BINDING PROTEIN / Calcium Binding Protein / Buffer / IMPase / EF-hand | ||||||
Function / homology | Function and homology information 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 / vitamin D binding / short-term memory ...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 / vitamin D binding / short-term memory / stereocilium / metanephric collecting duct development / presynaptic cytosol / regulation of long-term synaptic potentiation / postsynaptic cytosol / cellular response to organic substance / cochlea development / calyx of Held / GABA-ergic synapse / long-term memory / hippocampal mossy fiber to CA3 synapse / locomotory behavior / terminal bouton / dendritic spine / Amyloid fiber formation / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / extracellular exosome / zinc ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Noble, J.W. / Almalki, R. / Roe, S.M. / Wagner, A. / Dumanc, R. / Atack, J.R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: The X-ray structure of human calbindin-D28K: an improved model. Authors: Noble, J.W. / Almalki, R. / Roe, S.M. / Wagner, A. / Duman, R. / Atack, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fie.cif.gz | 109.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fie.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/6fie ftp://data.pdbj.org/pub/pdb/validation_reports/fi/6fie | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 30316.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CALB1, CAB27 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: P05937 | ||||
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#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SCN / | #4: 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: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Sample: 41.6mg/ml Calbindin-D28k in 1mM CaCl 5mM Tris pH8.0 (HCl). Reservoir: 0.1M Potassium thiocyanate and 30% w/v PEG 2000 MME. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 14, 2017 |
Radiation | Monochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→29.61 Å / Num. obs: 41505 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.024 / Rrim(I) all: 0.048 / Net I/av σ(I): 14.4 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.51→1.54 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.852 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2048 / CC1/2: 0.4 / Rpim(I) all: 0.506 / Rrim(I) all: 0.996 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: I23 Partial Model Resolution: 1.51→21.9 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.082
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Displacement parameters | Biso mean: 37.89 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.51→21.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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