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Yorodumi- PDB-8ah8: Crystal Structure of the third PDZ domain of PSD-95 protein in th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ah8 | |||||||||
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Title | Crystal Structure of the third PDZ domain of PSD-95 protein in the space group P3121 at pH 3.7 | |||||||||
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: 1.5 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 | 8ah8.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ah8.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 8ah8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/8ah8 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/8ah8 | HTTPS FTP |
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-Related structure data
Related structure data | 8ah4C 8ah5C 8ah6C 8ah7C 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11129.489 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: 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: 1.82 Å3/Da / Density % sol: 32.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.7 / 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: ID23-2 / Wavelength: 0.8731 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Feb 18, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→17.96 Å / Num. obs: 12949 / % possible obs: 96 % / Redundancy: 3.2 % / Biso Wilson estimate: 18.29 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.046 / Rrim(I) all: 0.086 / Net I/σ(I): 7.8 / Num. measured all: 41352 / Scaling rejects: 13 | ||||||||||||||||||||||||||||||
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: 1.5→17.96 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.08 / Phase error: 23.17 / 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: 58.17 Å2 / Biso mean: 24.2956 Å2 / Biso min: 6.04 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→17.96 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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