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Yorodumi- PDB-4hcn: Crystal structure of Burkholderia pseudomallei effector protein C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hcn | ||||||
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Title | Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin | ||||||
Components |
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Keywords | PROTEIN BINDING / UBIQUITIN/NEDD8 DEAMIDASE / UBIQUITIN / NEDD8 | ||||||
Function / homology | Function and homology information symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / modification-dependent protein catabolic process / protein tag activity / toxin activity / protein ubiquitination / host cell nucleus / ubiquitin protein ligase binding / extracellular region ...symbiont-mediated perturbation of host cell cycle progression / protein-glutamine glutaminase activity / protein-glutamine glutaminase / modification-dependent protein catabolic process / protein tag activity / toxin activity / protein ubiquitination / host cell nucleus / ubiquitin protein ligase binding / extracellular region / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Burkholderia pseudomallei (bacteria) Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Yao, Q. / Cui, J. / Zhu, Y. / Shao, F. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural mechanism of ubiquitin and NEDD8 deamidation catalyzed by bacterial effectors that induce macrophage-specific apoptosis. Authors: Yao, Q. / Cui, J. / Wang, J. / Li, T. / Wan, X. / Luo, T. / Gong, Y.N. / Xu, Y. / Huang, N. / Shao, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hcn.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hcn.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 4hcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hc/4hcn ftp://data.pdbj.org/pub/pdb/validation_reports/hc/4hcn | HTTPS FTP |
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-Related structure data
Related structure data | 4hcpC 1ubqS 3eirS C: citing same article (ref.) 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 28557.408 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 78-328 / Mutation: A156C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: K96243 / Gene: BPSS1385 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63KH5 |
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#2: Protein | Mass: 11097.469 Da / Num. of mol.: 1 / Fragment: unp RESIDUES 1-76 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: SCD2, UBI4, YLL039C / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0CG63 |
-Non-polymers , 4 types, 75 molecules
#3: Chemical | ChemComp-PEG / | ||||
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#4: Chemical | #5: Chemical | ChemComp-PO4 / | #6: 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: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.2 Details: 12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Monochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 10218 / % possible obs: 95.3 % / Observed criterion σ(I): 4 / Redundancy: 5.7 % |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY: 1UBQ AND PDB ENTRY: 3EIR Resolution: 2.6→19.35 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.856 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.66 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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