+Open data
-Basic information
Entry | Database: PDB / ID: 8c7d | |||||||||
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Title | Structure of the GEF Kalirin DH2 Domain | |||||||||
Components | Kalirin | |||||||||
Keywords | SIGNALING PROTEIN / GTPase exchange factor / helical bundle | |||||||||
Function / homology | Function and homology information regulation of small GTPase mediated signal transduction / extrinsic component of membrane / NRAGE signals death through JNK / RHOG GTPase cycle / RHOA GTPase cycle / ephrin receptor signaling pathway / vesicle-mediated transport / RAC1 GTPase cycle / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity ...regulation of small GTPase mediated signal transduction / extrinsic component of membrane / NRAGE signals death through JNK / RHOG GTPase cycle / RHOA GTPase cycle / ephrin receptor signaling pathway / vesicle-mediated transport / RAC1 GTPase cycle / EPHB-mediated forward signaling / guanyl-nucleotide exchange factor activity / axon guidance / MAPK6/MAPK4 signaling / G alpha (12/13) signalling events / actin cytoskeleton / nervous system development / G alpha (q) signalling events / postsynaptic density / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / extracellular exosome / nucleoplasm / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | |||||||||
Authors | Callens, M.C. / Thompson, A.P. / Gray, J.L. / Bountra, C. / von Delft, F. / Brennan, P.E. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: to be published Title: Structure-based alignment and analysis of RHO selectivity of RHO-DBL GTPase exchange factors Authors: Callens, M.C. / Thompson, A.P. / Gray, J.L. / von Delft, F. / Brennan, P.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c7d.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c7d.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 8c7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/8c7d ftp://data.pdbj.org/pub/pdb/validation_reports/c7/8c7d | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24059.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KALRN, DUET, DUO, HAPIP, TRAD / Production host: Escherichia coli (E. coli) References: UniProt: O60229, non-specific serine/threonine protein kinase |
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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: 2.13 Å3/Da / Density % sol: 42.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% W/V PEG3350, 0.1 M succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 18, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→59.76 Å / Num. obs: 17994 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 30.47 Å2 / CC1/2: 0.9976 / Rpim(I) all: 0.076 / Rrim(I) all: 0.261 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 881 / CC1/2: 0.351 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→59.76 Å / SU ML: 0.3656 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.2794 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 33.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→59.76 Å
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Refine LS restraints |
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LS refinement shell |
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