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Open data
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Basic information
Entry | Database: PDB / ID: 7xw1 | ||||||
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Title | The crystal structure of AhpD from Pseudomonas aeruginosa | ||||||
![]() | Carboxymuconolactone decarboxylase family protein | ||||||
![]() | OXIDOREDUCTASE / AhpD | ||||||
Function / homology | Alkylhydroperoxidase AhpD core / Carboxymuconolactone decarboxylase-like / Carboxymuconolactone decarboxylase family / AhpD-like / peroxiredoxin activity / Carboxymuconolactone decarboxylase family protein![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, B. | ||||||
Funding support | 1items
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![]() | ![]() Title: The crystal structure of AhpD from Pseudomonas aeruginosa Authors: Xu, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.6 KB | Display | ![]() |
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PDB format | ![]() | 42.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2o4dS S: Starting model for refinement |
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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
#1: Protein | Mass: 16246.528 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M Sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.36→19.88 Å / Num. obs: 7200 / % possible obs: 98.4 % / Redundancy: 19.8 % / Biso Wilson estimate: 55.63 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.27 / Rpim(I) all: 0.062 / Rrim(I) all: 0.277 / Net I/σ(I): 7.8 / Num. measured all: 142387 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2O4D Resolution: 2.36→19.88 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.08 / Stereochemistry target values: ML
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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 max: 149.07 Å2 / Biso mean: 67.1866 Å2 / Biso min: 29.81 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.36→19.88 Å
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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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