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- PDB-3eg5: Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP -
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Open data
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Basic information
Entry | Database: PDB / ID: 3eg5 | ||||||
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Title | Crystal structure of MDIA1-TSH GBD-FH3 in complex with CDC42-GMPPNP | ||||||
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Function / homology | ![]() RHO GTPases activate KTN1 / RHOV GTPase cycle / DCC mediated attractive signaling / negative regulation of neuron projection regeneration / multicellular organismal locomotion / CD28 dependent Vav1 pathway / RAC3 GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / RHOF GTPase cycle ...RHO GTPases activate KTN1 / RHOV GTPase cycle / DCC mediated attractive signaling / negative regulation of neuron projection regeneration / multicellular organismal locomotion / CD28 dependent Vav1 pathway / RAC3 GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / RHOF GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate PAKs / RHOB GTPase cycle / establishment or maintenance of apical/basal cell polarity / ERBB2 Regulates Cell Motility / RHOC GTPase cycle / CDC42 GTPase cycle / G beta:gamma signalling through CDC42 / GPVI-mediated activation cascade / RHOD GTPase cycle / EPHB-mediated forward signaling / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / EGFR downregulation / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lammers, M. / Meyer, S. / Kuehlmann, D. / Wittinghofer, A. | ||||||
![]() | ![]() Title: Specificity of Interactions between mDia Isoforms and Rho Proteins Authors: Lammers, M. / Meyer, S. / Kuhlmann, D. / Wittinghofer, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 214.5 KB | Display | ![]() |
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PDB format | ![]() | 169.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1z2cS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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Components
#1: Protein | Mass: 19802.719 Da / Num. of mol.: 2 / Fragment: UNP residues 1-178 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein | Mass: 44200.680 Da / Num. of mol.: 2 / Fragment: MDIAN-TSH, UNP residues 69-451 / Mutation: N164T, N165S, N166H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #3: Chemical | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.15 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: Bis-Tris-Propane (PH 8.8 adjusted with citric acid), 26% (w/v) PEG 3350, 250mM Na-Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2007 / Details: MIRRORS |
Radiation | Monochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→43.478 Å / Num. all: 38241 / Num. obs: 38038 / % possible obs: 99.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Rsym value: 0.084 / Net I/σ(I): 13.52 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 3.69 / Rsym value: 0.333 / % possible all: 99.8 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1Z2C Resolution: 2.7→43.47 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.101 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.986 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 53.029 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→43.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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