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Yorodumi- PDB-1ihj: Crystal Structure of the N-terminal PDZ domain of InaD in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ihj | ||||||
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Title | Crystal Structure of the N-terminal PDZ domain of InaD in complex with a NorpA C-terminal peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / intermolecular disulfide bond / PDZ domain | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Kimple, M.E. / Siderovski, D.P. / Sondek, J. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: Functional relevance of the disulfide-linked complex of the N-terminal PDZ domain of InaD with NorpA. Authors: Kimple, M.E. / Siderovski, D.P. / Sondek, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ihj.cif.gz | 54.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ihj.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 1ihj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ihj_validation.pdf.gz | 376.2 KB | Display | wwPDB validaton report |
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Full document | 1ihj_full_validation.pdf.gz | 380.4 KB | Display | |
Data in XML | 1ihj_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 1ihj_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ih/1ihj ftp://data.pdbj.org/pub/pdb/validation_reports/ih/1ihj | HTTPS FTP |
-Related structure data
Related structure data | 1be9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10771.533 Da / Num. of mol.: 2 / Fragment: PDZ1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: inaD / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24008 #2: Protein/peptide | Mass: 755.859 Da / Num. of mol.: 2 / Fragment: C-terminus / Source method: obtained synthetically Details: This peptide was chemically synthesized. It consists of the final seven residues of phospholipase C (gktefca). References: GenBank: 85099, phospholipase C #3: Water | ChemComp-HOH / | |
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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: 2.81 Å3/Da / Density % sol: 56.17 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000, lithium sulfate, glycerol, dithiothreitol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: used seeding | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.0072 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0072 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→20 Å / Num. all: 27241 / Num. obs: 25906 / % possible obs: 95.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.6 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.76→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.156 / % possible all: 86.7 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 86.7 % / Num. unique obs: 2424 / Mean I/σ(I) obs: 8.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1BE9 minus peptide Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 2 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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