+Open data
-Basic information
Entry | Database: PDB / ID: 1qvy | ||||||
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Title | Crystal structure of RhoGDI K(199,200)R double mutant | ||||||
Components | Rho GDP-dissociation inhibitor 1 | ||||||
Keywords | SIGNALING PROTEIN INHIBITOR / protein crystallization / rational surface mutagenesis / RhoGDI / high resolution / X-ray diffraction | ||||||
Function / homology | Function and homology information Rho GDP-dissociation inhibitor activity / regulation of synaptic vesicle cycle / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of Rho protein signal transduction / RHOC GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction ...Rho GDP-dissociation inhibitor activity / regulation of synaptic vesicle cycle / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of Rho protein signal transduction / RHOC GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / Rho protein signal transduction / immunological synapse / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC1 GTPase cycle / GTPase activator activity / Schaffer collateral - CA1 synapse / regulation of protein localization / cytoskeleton / negative regulation of apoptotic process / extracellular exosome / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Czepas, J. / Devedjiev, Y. / Krowarsh, D. / Derewenda, U. / Derewenda, Z.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: The impact of Lys-->Arg surface mutations on the crystallization of the globular domain of RhoGDI. Authors: Czepas, J. / Devedjiev, Y. / Krowarsch, D. / Derewenda, U. / Otlewski, J. / Derewenda, Z.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qvy.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qvy.ent.gz | 210.6 KB | Display | PDB format |
PDBx/mmJSON format | 1qvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qvy ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qvy | HTTPS FTP |
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-Related structure data
Related structure data | 1kmtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16025.268 Da / Num. of mol.: 4 / Fragment: C-terminal domain / Mutation: K(199,200)R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGST-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): XL-10 GOLD, EPICURIAN COLI BL21 / References: UniProt: P52565 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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: 2.19 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG 400, 0.1 M Tris, 0.2 M lithium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.919 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 3, 2002 / Details: monochromator , mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 84662 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KMT Resolution: 1.6→27.02 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.58 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.108 / ESU R Free: 0.086 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.983 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→27.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20 /
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