+Open data
-Basic information
Entry | Database: PDB / ID: 2ji0 | ||||||
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Title | CRYSTAL STRUCTURE OF RHOGDI K138Y, K141Y MUTANT | ||||||
Components | RHO GDP-DISSOCIATION INHIBITOR 1 | ||||||
Keywords | INHIBITOR / SURFACE ENTROPY REDUCTION / GTPASE ACTIVATION / CRYSTAL ENGINEERING | ||||||
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 / CDC42 GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / 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 / CDC42 GTPase cycle / RHOH GTPase cycle / semaphorin-plexin signaling pathway / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Cooper, D.R. / Boczek, T. / Derewenda, Z.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2007 Title: Protein Crystallization by Surface Entropy Reduction: Optimization of the Ser Strategy Authors: Cooper, D.R. / Boczek, T. / Grelewska, K. / Pinkowska, M. / Sikorska, M. / Zawadzki, M. / Derewenda, Z.S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ji0.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ji0.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ji0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ji0_validation.pdf.gz | 408.6 KB | Display | wwPDB validaton report |
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Full document | 2ji0_full_validation.pdf.gz | 410.3 KB | Display | |
Data in XML | 2ji0_validation.xml.gz | 5.4 KB | Display | |
Data in CIF | 2ji0_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2ji0 ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2ji0 | HTTPS FTP |
-Related structure data
Related structure data | 2bxwSC 2jhsC 2jhtC 2jhuC 2jhvC 2jhwC 2jhxC 2jhyC 2jhzC 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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Unit cell |
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-Components
#1: Protein | Mass: 15864.039 Da / Num. of mol.: 1 / Fragment: ISOPRENYL-BINDING DOMAIN, RESIDUES 66-201 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52565 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | MUTATIONS ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.3 % |
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Crystal grow | pH: 7.5 Details: 32% PEG 8000, 0.22M AMMONIUM SULFATE, 0.1 M SODIUM CACODYLATE PH6.5, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 5, 2005 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→2.18 Å / Num. obs: 5179 / % possible obs: 67.5 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.91 / % possible all: 22.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BXW Resolution: 2.1→37.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / SU B: 15.95 / SU ML: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.211 / ESU R Free: 0.309 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→37.14 Å
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Refine LS restraints |
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