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- PDB-8ah7: Crystal Structure of the third PDZ domain of PSD-95 protein in th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ah7 | ||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 protein in the space group P212121 at pH 4.0 | ||||||
![]() | cDNA FLJ50577, highly similar to Discs large homolog 4 | ||||||
![]() | PROTEIN BINDING / PDZ domain | ||||||
Function / homology | ![]() embryo development / AMPA glutamate receptor clustering / postsynaptic neurotransmitter receptor diffusion trapping / establishment or maintenance of epithelial cell apical/basal polarity / postsynaptic density membrane / neuromuscular junction / kinase binding / cell-cell adhesion / chemical synaptic transmission / basolateral plasma membrane / neuron projection Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | pH 4.0 P3112 polymorph | ||||||
![]() | Camara-Artigas, A. / Salinas-Garcia, M.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: pH-Driven Polymorphic Behaviour of the Third PDZ Domain of PSD95: The Role of Electrostatic Interactions Authors: Salinas-Garcia, M.C. / Plaza-Garrido, M. / Gavira, J.A. / Murciano-Calles, J. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Martinez, J.C. / Camara-Artigas, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.9 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.3 KB | Display | ![]() |
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Full document | ![]() | 422.3 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ah4C ![]() 8ah5C ![]() 8ah6C ![]() 8ah8C ![]() 6qjiS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 11148.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 30% PEG 4000, 0.2M Ammonium Sulfate, 0.1M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→19.53 Å / Num. obs: 24458 / % possible obs: 98.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 16.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.023 / Rrim(I) all: 0.05 / Net I/σ(I): 8.2 / Num. measured all: 99957 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QJI Resolution: 1.25→19.53 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.23 Å2 / Biso mean: 27.3931 Å2 / Biso min: 13.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→19.53 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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