+Open data
-Basic information
Entry | Database: PDB / ID: 2qkt | ||||||
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Title | Crystal Structure of the 5th PDZ domain of InaD | ||||||
Components | Inactivation-no-after-potential D protein | ||||||
Keywords | PEPTIDE BINDING PROTEIN / PDZ DOMAIN / SCAFFOLDING PROTEIN / DISULFIDE-BOND / Membrane / Sensory transduction / Vision / SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction ...myosin III binding / detection of light stimulus involved in sensory perception / inaD signaling complex / negative regulation of opsin-mediated signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / rhabdomere / cellular response to light stimulus / myosin binding / photoreceptor activity / phototransduction / visual perception / sensory perception of sound / protein localization / signaling receptor complex adaptor activity / calmodulin binding Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.05 Å | ||||||
Authors | Ranganathan, R. / Socolich, M. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007 Title: Dynamic Scaffolding in a G Protein-Coupled Signaling System. Authors: Mishra, P. / Socolich, M. / Wall, M.A. / Graves, J. / Wang, Z. / Ranganathan, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qkt.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qkt.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 2qkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qkt_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 2qkt_full_validation.pdf.gz | 430.3 KB | Display | |
Data in XML | 2qkt_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2qkt_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qk/2qkt ftp://data.pdbj.org/pub/pdb/validation_reports/qk/2qkt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is unknown. |
-Components
#1: Protein | Mass: 9711.200 Da / Num. of mol.: 2 / Fragment: 5th PDZ domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD / Plasmid: pGEX-5X-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.3M Sodium Citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection | Resolution: 2.05→20 Å / Num. obs: 14738 / % possible obs: 99.7 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 0.443 | |||||||||||||||||||||||||
Reflection shell | Resolution: 2.05→2.16 Å / Mean I/σ(I) obs: 16.7 / Rsym value: 0.153 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.05→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1082751.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 27.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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