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Yorodumi- PDB-8ah5: Crystal Structure of the third PDZ domain of PSD-95 protein in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ah5 | ||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 protein in the space group P212121 at pH 4.6 | ||||||
Components | cDNA FLJ50577, highly similar to Discs large homolog 4 | ||||||
Keywords | PROTEIN BINDING / PDZ domain | ||||||
Function / homology | Function and homology information neuromuscular junction / kinase binding / chemical synaptic transmission / neuron projection Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Model details | pH 4.0 P3112 polymorph | ||||||
Authors | Camara-Artigas, A. / Salinas Garcia, M.C. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Crystals / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ah5.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ah5.ent.gz | 55.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ah5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/8ah5 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ah5 | HTTPS FTP |
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-Related structure data
Related structure data | 8ah4C 8ah6C 8ah7C 8ah8C 6qjiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7Z4H2 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 30% PEG4K, 0.2M AMSO4, 0.1M AcONa |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 18, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→19.35 Å / Num. obs: 22582 / % possible obs: 95.6 % / Redundancy: 10.7 % / Biso Wilson estimate: 10.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.04 / Rrim(I) all: 0.136 / Net I/σ(I): 9.9 / Num. measured all: 242181 / Scaling rejects: 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6QJI Resolution: 1.25→19.35 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 21.3 / 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: 44.86 Å2 / Biso mean: 14.3678 Å2 / Biso min: 6.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→19.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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