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- PDB-8wdq: Crystal Structure of Pseudomonas aeruginosa SuhB in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8wdq | ||||||
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Title | Crystal Structure of Pseudomonas aeruginosa SuhB in complex with D-myo-inositol-1-phosphate | ||||||
![]() | Nus factor SuhB | ||||||
![]() | HYDROLASE / Inositol monophosphatase / SuhB / Pseudomonas aeruginosa / D-myo-inositol-1-phosphate | ||||||
Function / homology | ![]() inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphatidylinositol phosphate biosynthetic process / transcription antitermination / ribosome biogenesis / signal transduction / RNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yadav, V.K. / Maji, S. / Shukla, M. / Bhattacharyya, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of Pseudomonas aeruginosa SuhB in complex with D-myo-inositol-1-phosphate Authors: Yadav, V.K. / Maji, S. / Shukla, M. / Bhattacharyya, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.5 KB | Display | ![]() |
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PDB format | ![]() | 188.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 38.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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, 2 molecules AB
#1: Protein | Mass: 29668.654 Da / Num. of mol.: 2 / Mutation: F71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 312 molecules 














#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEO / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-DTU / ( | #7: Chemical | #8: Chemical | ChemComp-CA / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Sodium acetate trihydrate/acetate buffer, PEG 3350, pH 4.5 Temp details: Room temeperature |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 29, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→54.48 Å / Num. obs: 29259 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 20.61 Å2 / CC1/2: 0.988 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.9 % / Num. unique obs: 4112 / CC1/2: 0.866 / % possible all: 97.5 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→52.75 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: -25.1634084871 Å / Origin y: 11.8341978028 Å / Origin z: -31.4932678439 Å
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Refinement TLS group | Selection details: all |