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Yorodumi- PDB-5mr1: Crystal structure of the Pleckstrin homology domain of Interactor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mr1 | ||||||
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Title | Crystal structure of the Pleckstrin homology domain of Interactor protein for cytohesin exchange factors 1 (IPCEF1) | ||||||
Components | Interactor protein for cytohesin exchange factors 1 | ||||||
Keywords | SIGNALING PROTEIN / cytohesin / scaffold protein / Pleckstrin homology / PIP3E | ||||||
Function / homology | Function and homology information oxygen transport / oxygen carrier activity / peroxidase activity / response to oxidative stress / protein domain specific binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Newman, J.A. / Aitkenhead, H. / Wang, D. / Burgess-Brown, N. / Williams, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To be published Title: Crystal structure of the Pleckstrin homology domain of Interactor protein for cytohesin exchange factors 1 (IPCEF1) Authors: Newman, J.A. / Aitkenhead, H. / Wang, D. / Burgess-Brown, N. / Williams, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / Gileadi, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mr1.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mr1.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mr1_validation.pdf.gz | 410.6 KB | Display | wwPDB validaton report |
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Full document | 5mr1_full_validation.pdf.gz | 410.7 KB | Display | |
Data in XML | 5mr1_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 5mr1_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mr1 ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mr1 | HTTPS FTP |
-Related structure data
Related structure data | 1upqS 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: 12059.927 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: First two residues remain after cleavage of purificaiton tag Source: (gene. exp.) Homo sapiens (human) / Gene: IPCEF1, KIAA0403 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q8WWN9 |
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#2: 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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.2 M Lithium Sulfate, 25% PEG 3350, 0.1 M Bis Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→27.96 Å / Num. obs: 35945 / % possible obs: 97.2 % / Redundancy: 13.4 % / Biso Wilson estimate: 17.125 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1.593 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.551 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1upq Resolution: 1.2→26.9 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→26.9 Å
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Refine LS restraints |
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LS refinement shell |
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