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- PDB-8gkd: Crystal structure of the peptidoglycan O-acetylesterase Ape1 (ami... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gkd | ||||||
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Title | Crystal structure of the peptidoglycan O-acetylesterase Ape1 (amino acids 41-392) from Campylobacter jejuni | ||||||
![]() | SGNH hydrolase-type esterase domain-containing protein | ||||||
![]() | HYDROLASE / Peptidoglycan O-acetylesterase / SGNH hydrolase / CBM35 / product bound complex | ||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / ACETATE ION / SGNH hydrolase-type esterase domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lin, C.S. / Murphy, M.E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of the CBM35 domain in assisting catalysis by Ape1, a Campylobacter jejuni O-acetyl esterase Authors: Lin, C.S. / Yen, I.Y. / Chan, A.C. / Murphy, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 437.1 KB | Display | ![]() |
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PDB format | ![]() | 359.1 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 | ![]() | 43 KB | Display | |
Data in CIF | ![]() | 62.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gldC 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41012.312 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 81-176 / Gene: CJJ81176_0638 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.35 % / Description: rod-shaped crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 100 mM CAPS pH 10.5, 200 mM NaCl, 16% (w/v) PEG8000, 2.5% (w/v) PEG3350 |
-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: Dec 3, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 95429 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.045 / Rrim(I) all: 0.11 / Χ2: 0.921 / Net I/σ(I): 5.5 / Num. measured all: 546678 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso max: 146.07 Å2 / Biso mean: 27.5055 Å2 / Biso min: 13.31 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→34.86 Å
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LS refinement shell | Resolution: 1.8→1.87 Å
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