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- PDB-9biz: Crystal structure of the periplasmic domain of IgaA from Klebsiel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9biz | ||||||
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Title | Crystal structure of the periplasmic domain of IgaA from Klebsiella pneumoniae | ||||||
![]() | Intracellular growth attenuator protein igaA | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Watanabe, N. / Savchenko, A. / Center for Structural Biology of Infectious Diseases (CSBID) / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.2 KB | Display | ![]() |
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PDB format | ![]() | 94.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.9 KB | Display | ![]() |
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Full document | ![]() | 424.2 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9biyC ![]() 9bj0C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 29877.654 Da / Num. of mol.: 1 / Fragment: periplasmic domain (UNP residues 373-645) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.73 Å3/Da / Density % sol: 74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.0 M lithium sulfate, 0.1 M Bis-Tris, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 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: 2.5→50 Å / Num. obs: 17504 / % possible obs: 94.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 57.42 Å2 / Rpim(I) all: 0.103 / Net I/σ(I): 1.05 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 649 / CC1/2: 0.503 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 75.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 3.97628375098 Å / Origin y: 0.994053870875 Å / Origin z: 14.1195750345 Å
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Refinement TLS group | Selection details: all |