+Open data
-Basic information
Entry | Database: PDB / ID: 1fso | ||||||
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Title | CRYSTAL STRUCTURE OF TRUNCATED HUMAN RHOGDI QUADRUPLE MUTANT | ||||||
Components | RHO GDP-DISSOCIATION INHIBITOR 1 | ||||||
Keywords | SIGNALING PROTEIN INHIBITOR / immunoglobulin fold / beta sandwich motif / isoprenyl-binding domain / GDP-dissociation inhibitor of Rho GTPases | ||||||
Function / homology | Function and homology information Rho GDP-dissociation inhibitor activity / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of synaptic vesicle cycle / regulation of Rho protein signal transduction / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / semaphorin-plexin signaling pathway / RHOH GTPase cycle ...Rho GDP-dissociation inhibitor activity / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of synaptic vesicle cycle / regulation of Rho protein signal transduction / RHOC GTPase cycle / CDC42 GTPase cycle / Rho protein signal transduction / semaphorin-plexin signaling pathway / RHOH GTPase cycle / 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 / Resolution: 2 Å | ||||||
Authors | Longenecker, K.L. / Garrard, S.M. / Sheffield, P.J. / Derewenda, Z.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Authors: Longenecker, K.L. / Garrard, S.M. / Sheffield, P.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 | 1fso.cif.gz | 43.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fso.ent.gz | 30.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/1fso ftp://data.pdbj.org/pub/pdb/validation_reports/fs/1fso | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The monomer of the asymmetric unit is the biologically active species |
-Components
#1: Protein | Mass: 15828.947 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN / Mutation: K135A, K138A, K141A, L196F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Production host: Escherichia coli (E. coli) / References: UniProt: P52565 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.85 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ammonium sulfate and MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS 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: NSLS / Beamline: X9B / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. all: 20565 / Num. obs: 20565 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.305 / Num. unique all: 2025 / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 83504 |
Reflection shell | *PLUS Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Resolution: 2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.216 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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