+Open data
-Basic information
Entry | Database: PDB / ID: 7de7 | ||||||
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Title | Crystal structure of PDZD7 HHD domain | ||||||
Components | PDZ domain-containing protein 7 | ||||||
Keywords | LIPID BINDING PROTEIN / PDZD7 / HHD domain / membrane-targeting | ||||||
Function / homology | Function and homology information USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / stereocilium / auditory receptor cell stereocilium organization / establishment of localization in cell ...USH2 complex / stereocilia ankle link / inner ear receptor cell differentiation / stereocilia ankle link complex / stereocilium tip / detection of mechanical stimulus involved in sensory perception of sound / auditory receptor cell development / stereocilium / auditory receptor cell stereocilium organization / establishment of localization in cell / sensory perception of sound / establishment of protein localization / cilium / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Wang, H. / Lin, L. / Lu, Q. | ||||||
Citation | Journal: Front Cell Dev Biol / Year: 2021 Title: Structure and Membrane Targeting of the PDZD7 Harmonin Homology Domain (HHD) Associated With Hearing Loss. Authors: Lin, L. / Wang, H. / Ren, D. / Xia, Y. / He, G. / Lu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7de7.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7de7.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 7de7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7de7_validation.pdf.gz | 753.9 KB | Display | wwPDB validaton report |
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Full document | 7de7_full_validation.pdf.gz | 754.1 KB | Display | |
Data in XML | 7de7_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 7de7_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/7de7 ftp://data.pdbj.org/pub/pdb/validation_reports/de/7de7 | HTTPS FTP |
-Related structure data
Related structure data | 6fddS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 11761.536 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdzd7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: E9Q9W7 #2: Chemical | ChemComp-2Q5 / ( | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.73 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris pH 6.5, 45% Polypropylene glycol P400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 4, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.49→37.5 Å / Num. obs: 32592 / % possible obs: 99.4 % / Redundancy: 6.74 % / Biso Wilson estimate: 25.745 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.091 / Χ2: 0.819 / Net I/σ(I): 13.49 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FDD Resolution: 1.49→37.5 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.07 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.51 Å2 / Biso mean: 22.9697 Å2 / Biso min: 11.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→37.5 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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