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Yorodumi- PDB-3odx: Crystal Structure of an N-terminally Truncated Linker-DH/PH Domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3odx | ||||||
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Title | Crystal Structure of an N-terminally Truncated Linker-DH/PH Domains of p115-RhoGEF | ||||||
Components | Rho guanine nucleotide exchange factor 1 | ||||||
Keywords | SIGNALING PROTEIN / regulation of RhoA GTPase / RhoGEF / DH / PH / Rho | ||||||
Function / homology | Function and homology information regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events ...regulation of small GTPase mediated signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / RHOC GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / GTPase activator activity / guanyl-nucleotide exchange factor activity / G protein-coupled receptor binding / G alpha (12/13) signalling events / G protein-coupled receptor signaling pathway / RNA binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Chen, Z. / Guo, L. / Sprang, S.R. / Sternweis, P.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2011 Title: Modulation of a GEF switch: Autoinhibition of the intrinsic guanine nucleotide exchange activity of p115-RhoREF Authors: Chen, Z. / Guo, L. / Sprang, S.R. / Sternweis, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3odx.cif.gz | 292.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3odx.ent.gz | 240.3 KB | Display | PDB format |
PDBx/mmJSON format | 3odx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/3odx ftp://data.pdbj.org/pub/pdb/validation_reports/od/3odx | HTTPS FTP |
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-Related structure data
Related structure data | 3odoSC 3odwC 3p6aC 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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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
#1: Protein | Mass: 48091.949 Da / Num. of mol.: 2 / Fragment: UNP residues 353-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF1 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92888 |
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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: 3.65 Å3/Da / Density % sol: 66.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 15-18% PEG 3350, 0.2M sodium chloride, and 0.1M NaHEPES, pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K PH range: 6.2-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 20, 2010 / Details: Mirrors |
Radiation | Monochromator: Double-crystal Si-111 & Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 22503 / % possible obs: 99.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ODO Resolution: 3.2→48.9 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 52.311 / SU ML: 0.392 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.37 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→48.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2785 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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