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Yorodumi- PDB-9bj0: Crystal structure of the periplasmic domain of IgaA from Escheric... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bj0 | ||||||
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Title | Crystal structure of the periplasmic domain of IgaA from Escherichia coli | ||||||
Components | Intracellular growth attenuator protein igaA | ||||||
Keywords | SIGNALING PROTEIN / Periplasmic protein / signal transduction / Structural Genomics / Center for Structural Biology of Infectious Diseases / CSBID / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Intracellular growth attenuator IgaA / Intracellular growth attenuator protein IgaA / plasma membrane / Intracellular growth attenuator protein igaA Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Watanabe, N. / Savchenko, A. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2024 Title: Molecular insights into the initiation step of the Rcs signaling pathway. Authors: Watanabe, N. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bj0.cif.gz | 122.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bj0.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 9bj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bj0_validation.pdf.gz | 434.9 KB | Display | wwPDB validaton report |
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Full document | 9bj0_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 9bj0_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 9bj0_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/9bj0 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/9bj0 | HTTPS FTP |
-Related structure data
Related structure data | 9biyC 9bizC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29556.217 Da / Num. of mol.: 2 / Fragment: periplasmic domain (UNP residues 203-475) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GP975_16005 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8T5ZEU4 #2: 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: 2.88 Å3/Da / Density % sol: 57.32 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: 20% PEG3350, 0.2 M potassium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→40 Å / Num. obs: 20383 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 74.17 Å2 / Rrim(I) all: 0.083 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2.65→2.74 Å / Num. unique obs: 1993 / CC1/2: 0.788 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→39.36 Å / SU ML: 0.3385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7673 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 81.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→39.36 Å
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Refine LS restraints |
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LS refinement shell |
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