+Open data
-Basic information
Entry | Database: PDB / ID: 4mit | ||||||
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Title | Crystal structure of E. histolytica RacC bound to the EhPAK4 PBD | ||||||
Components |
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Keywords | SIGNALING PROTEIN / G domain / p21 binding domain / CRIB motif / hydrolase / kinase / GTP binding | ||||||
Function / homology | Function and homology information small GTPase-mediated signal transduction / GTPase activity / protein serine/threonine kinase activity / GTP binding / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Entamoeba histolytica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Bosch, D.E. / Siderovski, D.P. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: Entamoeba histolytica RacC Selectively Engages p21-Activated Kinase Effectors. Authors: Bosch, D.E. / Siderovski, D.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mit.cif.gz | 196.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mit.ent.gz | 156.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/4mit ftp://data.pdbj.org/pub/pdb/validation_reports/mi/4mit | HTTPS FTP |
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-Related structure data
Related structure data | 3th5S 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: 20645.807 Da / Num. of mol.: 4 / Mutation: Q65L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EhRacC, KM1_331620 / Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: M7WE85, UniProt: Q24816*PLUS, small monomeric GTPase #2: Protein | Mass: 7505.105 Da / Num. of mol.: 4 / Fragment: EhPAK4 PBD, unp residues 33-99 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI7A_018700, EhPAK4 / Plasmid: pLIC His / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: N9UZ59 #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: 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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: EhRacC-GTP/EhPAK4 PBD complex was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 4000, 200 mM magnesium chloride, and 100 mM MES, pH 6.5, VAPOR ...Details: EhRacC-GTP/EhPAK4 PBD complex was mixed 1:1 with and equilibrated against crystallization solution containing 22% (w/v) PEG 4000, 200 mM magnesium chloride, and 100 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 14, 2013 / Details: custom |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→46.9 Å / Num. all: 41369 / Num. obs: 36818 / % possible obs: 89 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 34.7 |
Reflection shell | Resolution: 2.35→2.37 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 2.8 / Num. unique all: 910 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TH5 Resolution: 2.35→46.896 Å / SU ML: 0.28 / σ(F): 1.39 / Phase error: 26.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→46.896 Å
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Refine LS restraints |
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LS refinement shell |
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