+Open data
-Basic information
Entry | Database: PDB / ID: 1nty | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the first DH/PH domain of Trio to 1.7 A | ||||||
Components | Triple functional domain protein | ||||||
Keywords | SIGNALING PROTEIN / Dbl / Pleckstrin / GEF / Rho / GTPase / Guanine-nucleotide releasing factor / Phosphorylation | ||||||
Function / homology | Function and homology information cell surface receptor protein tyrosine phosphatase signaling pathway / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / negative regulation of fat cell differentiation / extrinsic component of membrane / presynaptic active zone / postsynaptic modulation of chemical synaptic transmission / NRAGE signals death through JNK / RHOJ GTPase cycle / CDC42 GTPase cycle ...cell surface receptor protein tyrosine phosphatase signaling pathway / DCC mediated attractive signaling / regulation of small GTPase mediated signal transduction / negative regulation of fat cell differentiation / extrinsic component of membrane / presynaptic active zone / postsynaptic modulation of chemical synaptic transmission / NRAGE signals death through JNK / RHOJ GTPase cycle / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / neuron projection morphogenesis / cell projection / axon guidance / G alpha (12/13) signalling events / G alpha (q) signalling events / postsynapse / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molecular Replacement followed by ARP/wARP / Resolution: 1.7 Å | ||||||
Authors | Skowronek, K.R. / Zheng, Y. / Nassar, N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The C-terminal basic tail of RhoG assists the guanine nucleotide exchange factor trio in binding to phospholipids. Authors: Skowronek, K.R. / Guo, F. / Zheng, Y. / Nassar, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nty.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nty.ent.gz | 64 KB | Display | PDB format |
PDBx/mmJSON format | 1nty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/1nty ftp://data.pdbj.org/pub/pdb/validation_reports/nt/1nty | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 36431.746 Da / Num. of mol.: 1 / Fragment: N-terminal DH/PH domains, residues 1225-1535 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TRIO / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O75962 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.12 % |
---|---|
Crystal grow | Temperature: 277 K / Method: batch method. / pH: 7.5 / Details: DTT, pH 7.5, Batch Method., temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 22, 2002 / Details: Monochromator |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 56048 / % possible obs: 90.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.8 % / Biso Wilson estimate: 23.9 Å2 / Rsym value: 0.088 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.412 / % possible all: 55.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: Molecular Replacement followed by ARP/wARP Resolution: 1.7→19.82 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 16641310.83 / Data cutoff high rms absF: 16641310.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0112 Å2 / ksol: 0.406473 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→19.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|