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Open data
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Basic information
Entry | Database: PDB / ID: 8acr | ||||||
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Title | Structure of Pseudomonas aeruginosa aminopeptidase, PaAP | ||||||
![]() | Keratinase KP1 | ||||||
![]() | HYDROLASE / E340A mutant / Full-length | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harding, C.J. / Czekster, C.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. aeruginosa. Authors: Harding, C.J. / Bischoff, M. / Bergkessel, M. / Czekster, C.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.6 KB | Display | ![]() |
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PDB format | ![]() | 160.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 326.5 KB | Display | ![]() |
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Full document | ![]() | 327.1 KB | Display | |
Data in XML | ![]() | 13.8 KB | Display | |
Data in CIF | ![]() | 18.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ac7SC ![]() 8ac9C ![]() 8acgC ![]() 8ackC 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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Unit cell |
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Components
#1: Protein | Mass: 54882.883 Da / Num. of mol.: 1 / Mutation: E340A Source method: isolated from a genetically manipulated source Details: Truncation construct / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M MMT (DL-Malic acid, MES monohydrate, Tris) pH 6.0, 25 % w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 10, 2022 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→52.75 Å / Num. obs: 32511 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 47.07 Å2 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Net I/σ(I): 21.7 / Num. measured all: 428078 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 8AC7 Resolution: 2.1→46.017 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.9 / 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: 116.99 Å2 / Biso mean: 55.3543 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→46.017 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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