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Yorodumi- PDB-4hzb: Crystal structure of the type VI SeMet effector-immunity complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hzb | ||||||
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Title | Crystal structure of the type VI SeMet effector-immunity complex Tae3-Tai3 from Ralstonia pickettii | ||||||
Components |
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Keywords | HYDROLASE / protein-protein complex / alpha+beta / endopeptidase / periplasmic space | ||||||
Function / homology | Function and homology information Domain of unknown function DUF3828 / Protein of unknown function (DUF3828) / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Ralstonia pickettii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Dong, C. / Zhang, H. / Gao, Z.Q. / Dong, Y.H. | ||||||
Citation | Journal: Biochem.J. / Year: 2013 Title: Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3 Authors: Dong, C. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / She, Z. / Liu, G.F. / Shen, Y.Q. / Su, X.D. / Dong, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hzb.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hzb.ent.gz | 124.5 KB | Display | PDB format |
PDBx/mmJSON format | 4hzb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hzb_validation.pdf.gz | 475 KB | Display | wwPDB validaton report |
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Full document | 4hzb_full_validation.pdf.gz | 481.8 KB | Display | |
Data in XML | 4hzb_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 4hzb_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/4hzb ftp://data.pdbj.org/pub/pdb/validation_reports/hz/4hzb | HTTPS FTP |
-Related 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: 13241.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3261 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF2 #2: Protein | Mass: 17311.689 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3260 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF3 #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: 2.7 Å3/Da / Density % sol: 54.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.01M ferric chloride hexahydrate, 0.1M tri-sodium citrate dihydrate pH5.6, 10% v/v jeffamine M-600 , pH 5.6 , VAPOR DIFFUSION, SITTING DROP, temperature 277 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 32353 / Num. obs: 32299 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 27.08 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1529 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→35.054 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8081 / SU ML: 0.38 / σ(F): 5.59 / Phase error: 25.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.065 Å2 / ksol: 0.337 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.77 Å2 / Biso mean: 28.4819 Å2 / Biso min: 6.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→35.054 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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