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Yorodumi- PDB-1gwn: The crystal structure of the core domain of RhoE/Rnd3 - a constit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gwn | ||||||
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Title | The crystal structure of the core domain of RhoE/Rnd3 - a constitutively activated small G protein | ||||||
Components | Rho-related GTP-binding protein RhoE | ||||||
Keywords | GTPASE / INACTIVE GTPASE / SIGNAL TRANSDUCTION | ||||||
Function / homology | Function and homology information cortical cytoskeleton organization / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / actin filament organization / cell projection / regulation of actin cytoskeleton organization / cell migration / regulation of cell shape / cell cortex / actin cytoskeleton organization ...cortical cytoskeleton organization / establishment or maintenance of cell polarity / small GTPase-mediated signal transduction / actin filament organization / cell projection / regulation of actin cytoskeleton organization / cell migration / regulation of cell shape / cell cortex / actin cytoskeleton organization / cytoplasmic vesicle / vesicle / cytoskeleton / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / GTP binding / protein kinase binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Garavini, H. / Riento, K. / Phelan, J.P. / McAlister, M.S.B. / Ridley, A.J. / Keep, N.H. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal Structure of the Core Domain of Rhoe/Rnd3: A Constitutively Activated Small G Protein Authors: Garavini, H. / Riento, K. / Phelan, J.P. / McAlister, M.S.B. / Ridley, A.J. / Keep, N.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gwn.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gwn.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gwn_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1gwn_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1gwn_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1gwn_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/1gwn ftp://data.pdbj.org/pub/pdb/validation_reports/gw/1gwn | HTTPS FTP |
-Related structure data
Related structure data | 1cxzS S: Starting model for refinement |
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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 oper: (Code: given Matrix: (0.978372, -0.026484, 0.205153), Vector: |
-Components
#1: Protein | Mass: 22862.746 Da / Num. of mol.: 2 / Fragment: CORE DOMAIN, RESIDUES 16-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnd3, Arhe, Rhoe / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61588 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | RESIDUES 1-15 AND 201 ONWARDS HAVE BEEN DELETED. THE N-TERMINUS INCLUDES AN UNCLEAVED HIS-TAG. | |
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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: 2.25 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 0.1M HEPES PH 7.5, 10% PROPAN-2-OL, 20% PEG 4000 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→18.8 Å / Num. obs: 25276 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 115552 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 3592 / Num. measured obs: 15240 / Mean I/σ(I) obs: 3.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CXZ CHAIN A Resolution: 2.1→18.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.871 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY IN THE REGION OF RESIDUE 23 IS AMBIGUOUS AND THE CIS-CONFORMATION OF LYS23 MAY BE DUE TO THE POOR DEFINITION OF THE ENCLOSING DENSITY.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→18.8 Å
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Refine LS restraints |
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