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Open data
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Basic information
Entry | Database: PDB / ID: 7xp1 | ||||||
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Title | Crystal structure of PmiR from Pseudomonas aeruginosa | ||||||
![]() | Probable transcriptional regulator | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y.X. / Liang, H.H. / Gan, J.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: PmiR senses 2-methylisocitrate levels to regulate bacterial virulence in Pseudomonas aeruginosa. Authors: Cui, G. / Zhang, Y. / Xu, X. / Liu, Y. / Li, Z. / Wu, M. / Liu, J. / Gan, J. / Liang, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7xp0SC S: Starting model for refinement 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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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25027.408 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 12 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MIC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MIC.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-MIC / | ||||
#4: Chemical | ![]() #5: Chemical | ChemComp-GOL / | ![]() #6: Water | ChemComp-HOH / | ![]() |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % / Description: block |
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Crystal grow![]() | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: MES/Sodium hydroxide, Magnesium sulfate / PH range: 5.6-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→30 Å / Num. obs: 9006 / % possible obs: 96.4 % / Redundancy: 17.7 % / Biso Wilson estimate: 30.55 Å2 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.01 / Rrim(I) all: 0.048 / Χ2: 0.971 / Net I/σ(I): 11.4 / Num. measured all: 159703 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7XP0 Resolution: 2.5→29.22 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 26.28 / Stereochemistry target values: ML
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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: 129.71 Å2 / Biso mean: 47.4535 Å2 / Biso min: 10.82 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→29.22 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3
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Refinement TLS params. | Method: refined / Origin x: 4.5557 Å / Origin y: 10.8511 Å / Origin z: -23.2557 Å
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Refinement TLS group |
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