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Yorodumi- PDB-8gkv: Crystal structure of anti-adaptor IraP that regulates RpoS proteolysis -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gkv | ||||||
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Title | Crystal structure of anti-adaptor IraP that regulates RpoS proteolysis | ||||||
Components | Anti-adapter protein IraP | ||||||
Keywords | GENE REGULATION / alpha helix | ||||||
Function / homology | Sigma-S stabilisation anti-adaptor protein / Sigma-S stabilisation anti-adaptor protein / anti-sigma factor antagonist activity / cellular response to phosphate starvation / negative regulation of protein catabolic process / cytoplasm / Anti-adapter protein IraP Function and homology information | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.351 Å | ||||||
Model details | Leucine zipper-like protein | ||||||
Authors | Shaw, G.X. / Gan, J. / Suburaman, P. / Battesti, A. / Zhou, Y.N. / Wickner, S. / Gottesman, S. / Ji, X. | ||||||
Funding support | United States, 1items
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Citation | Journal: to be published Title: Structural and functional study of anti-adaptor IraP-mediated regulation of RpoS proteolysis Authors: Tripathi, A. / Hoskins, J. / Shaw, G.X. / Gan, J. / Tong, S. / Battesti, A. / Jenkins, L.M. / Ji, X. / Wickner, S. / Gottesman, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gkv.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gkv.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 8gkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gkv_validation.pdf.gz | 471.8 KB | Display | wwPDB validaton report |
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Full document | 8gkv_full_validation.pdf.gz | 472.3 KB | Display | |
Data in XML | 8gkv_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 8gkv_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/8gkv ftp://data.pdbj.org/pub/pdb/validation_reports/gk/8gkv | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10048.501 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-86 / Mutation: C23S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: iraP, yaiB, b0382, JW0373 / Plasmid: IraPC23S / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AAN9 |
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-Non-polymers , 5 types, 43 molecules
#2: Chemical | ChemComp-EPE / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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 Å3/Da / Density % sol: 38.65 % / Mosaicity: 0.806 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tri-Na citrate, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: k+l,h+l,-l / Fraction: 0.17 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→30 Å / Num. obs: 6391 / % possible obs: 95.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Χ2: 1.093 / Net I/σ(I): 16 / Num. measured all: 21575 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.351→29.064 Å / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.48 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.6 Å2 / Biso mean: 55.296 Å2 / Biso min: 21.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.351→29.064 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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