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Yorodumi- PDB-4qam: Crystal Structure of the RPGR RCC1-like domain in complex with th... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qam | ||||||
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Title | Crystal Structure of the RPGR RCC1-like domain in complex with the RPGR-interacting domain of RPGRIP1 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / type II C2 domain / beta propeller | ||||||
Function / homology | Function and homology information photoreceptor distal connecting cilium / response to stimulus / intraciliary transport / photoreceptor connecting cilium / eye photoreceptor cell development / neural precursor cell proliferation / axoneme / photoreceptor outer segment / cilium assembly / sperm flagellum ...photoreceptor distal connecting cilium / response to stimulus / intraciliary transport / photoreceptor connecting cilium / eye photoreceptor cell development / neural precursor cell proliferation / axoneme / photoreceptor outer segment / cilium assembly / sperm flagellum / visual perception / ciliary basal body / guanyl-nucleotide exchange factor activity / intracellular protein transport / ubiquitin protein ligase activity / retina development in camera-type eye / ubiquitin-dependent protein catabolic process / protein ubiquitination / centrosome / Golgi apparatus / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Remans, K. / Buerger, M. / Vetter, I.R. / Wittinghofer, A. | ||||||
Citation | Journal: Cell Rep / Year: 2014 Title: C2 domains as protein-protein interaction modules in the ciliary transition zone. Authors: Remans, K. / Burger, M. / Vetter, I.R. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qam.cif.gz | 238.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qam.ent.gz | 188.3 KB | Display | PDB format |
PDBx/mmJSON format | 4qam.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qam_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 4qam_full_validation.pdf.gz | 471.9 KB | Display | |
Data in XML | 4qam_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 4qam_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qam ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qam | HTTPS FTP |
-Related structure data
Related structure data | 4jhnS 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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Unit cell |
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-Components
#1: Protein | Mass: 43553.012 Da / Num. of mol.: 1 / Fragment: RCC1-like domain (UNP residues 1-392) / Mutation: V195I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RP3, RPGR, XLRP3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92834 | ||||
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#2: Protein | Mass: 23185.064 Da / Num. of mol.: 1 / Fragment: RPGR-interacting domain (UNP residues 1091-1286) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RPGRIP1 / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL / References: UniProt: Q96KN7 | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG3350, 300 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97948 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.83→43.232 Å / Num. obs: 58347 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.282 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JHN Resolution: 1.83→43.23 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1837 / WRfactor Rwork: 0.1504 / Occupancy max: 1 / Occupancy min: 0.48 / FOM work R set: 0.8867 / SU B: 4.667 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1073 / SU Rfree: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.05 Å2 / Biso mean: 32.961 Å2 / Biso min: 9.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.83→43.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.83→1.878 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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