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Open data
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Basic information
Entry | Database: PDB / ID: 5m6c | ||||||
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Title | CRYSTAL STRUCTURE OF T71N MUTANT OF HUMAN HIPPOCALCIN | ||||||
![]() | (Neuron-specific calcium-binding protein hippocalcin) x 2 | ||||||
![]() | CALCIUM BINDING PROTEIN | ||||||
Function / homology | ![]() response to Aroclor 1254 / response to ketamine / regulation of voltage-gated calcium channel activity / cellular response to electrical stimulus / cellular response to L-glutamate / regulation of postsynaptic neurotransmitter receptor internalization / neuronal cell body membrane / dendritic spine head / inner ear development / positive regulation of protein targeting to membrane ...response to Aroclor 1254 / response to ketamine / regulation of voltage-gated calcium channel activity / cellular response to electrical stimulus / cellular response to L-glutamate / regulation of postsynaptic neurotransmitter receptor internalization / neuronal cell body membrane / dendritic spine head / inner ear development / positive regulation of protein targeting to membrane / dendrite membrane / cellular response to calcium ion / dendrite cytoplasm / calcium-mediated signaling / kinase binding / retina development in camera-type eye / actin binding / perikaryon / axon / glutamatergic synapse / calcium ion binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Helassa, N. / Antonyuk, S.V. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biophysical and functional characterization of hippocalcin mutants responsible for human dystonia. Authors: Helassa, N. / Antonyuk, S.V. / Lian, L.Y. / Haynes, L.P. / Burgoyne, R.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.4 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.1 KB | Display | ![]() |
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Full document | ![]() | 436.6 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5g4pSC ![]() 5g58C 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 7 - 187 / Label seq-ID: 7 - 187
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Components
#1: Protein | Mass: 22466.402 Da / Num. of mol.: 1 / Mutation: T71N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 22496.428 Da / Num. of mol.: 1 / Mutation: T71N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.5, 18% V/V 2-PROPANOL, 16% W/V PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3→47.3 Å / Num. obs: 8283 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 62 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.122 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 3→3.18 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.31 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5g4p Resolution: 3→47.3 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.861 / SU B: 31.597 / SU ML: 0.551 / Cross valid method: THROUGHOUT / ESU R Free: 0.538 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.297 Å2
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Refinement step | Cycle: 1 / Resolution: 3→47.3 Å
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Refine LS restraints |
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