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Yorodumi- PDB-3p6a: Crystal Structure of the DH/PH domains of p115-RhoGEF (R399E mutant) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p6a | ||||||
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Title | Crystal Structure of the DH/PH domains of p115-RhoGEF (R399E mutant) | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 3p6a.cif.gz | 291.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p6a.ent.gz | 239.6 KB | Display | PDB format |
PDBx/mmJSON format | 3p6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p6a_validation.pdf.gz | 442.1 KB | Display | wwPDB validaton report |
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Full document | 3p6a_full_validation.pdf.gz | 459.7 KB | Display | |
Data in XML | 3p6a_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 3p6a_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/3p6a ftp://data.pdbj.org/pub/pdb/validation_reports/p6/3p6a | HTTPS FTP |
-Related structure data
Related structure data | 3odoSC 3odwC 3odxC 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: 43911.664 Da / Num. of mol.: 2 / Fragment: UNP residues 377-748 / Mutation: R399E 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: 3.98 Å3/Da / Density % sol: 69.08 % |
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Crystal grow | Temperature: 293 K Details: 2.7-3.0M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 8, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 46979 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ODO Resolution: 2.5→48.3 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.785 / SU ML: 0.187 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.241 / 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: 48.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.3 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: 2824 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.56 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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