+Open data
-Basic information
Entry | Database: PDB / ID: 7csp | ||||||
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Title | Structure of Ephexin4 IDPSH | ||||||
Components | Rho guanine nucleotide exchange factor 16 | ||||||
Keywords | SIGNALING PROTEIN / Ephexin4 / GEF / Autoinhibition | ||||||
Function / homology | Function and homology information CDC42 GTPase cycle / NRAGE signals death through JNK / RHOG GTPase cycle / G alpha (12/13) signalling events / activation of GTPase activity / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / positive regulation of protein localization to plasma membrane / receptor tyrosine kinase binding ...CDC42 GTPase cycle / NRAGE signals death through JNK / RHOG GTPase cycle / G alpha (12/13) signalling events / activation of GTPase activity / cell chemotaxis / guanyl-nucleotide exchange factor activity / PDZ domain binding / positive regulation of protein localization to plasma membrane / receptor tyrosine kinase binding / small GTPase binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Zhang, M. / Lin, L. / Wang, C. / Zhu, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Double inhibition and activation mechanisms of Ephexin family RhoGEFs. Authors: Zhang, M. / Lin, L. / Wang, C. / Zhu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7csp.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7csp.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 7csp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/7csp ftp://data.pdbj.org/pub/pdb/validation_reports/cs/7csp | HTTPS FTP |
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-Related structure data
Related structure data | 7csoSC 7csrC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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-Components
#1: Protein | Mass: 57456.906 Da / Num. of mol.: 2 / Mutation: 242-252 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgef16 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q3U5C8 |
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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: 3.56 Å3/Da / Density % sol: 65.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 2.8 M Sodium acetate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 13, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→46.83 Å / Num. obs: 59938 / % possible obs: 94.8 % / Redundancy: 3.688 % / Biso Wilson estimate: 80.826 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.104 / Χ2: 0.867 / Net I/σ(I): 10.35 / Num. measured all: 221044 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CSO Resolution: 3→46.83 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.87 / 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: 204.02 Å2 / Biso mean: 88.2665 Å2 / Biso min: 36.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→46.83 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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