+Open data
-Basic information
Entry | Database: PDB / ID: 5txc | ||||||
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Title | AtxE2 Isopeptidase - APO | ||||||
Components | AtxE2 | ||||||
Keywords | HYDROLASE / Lasso Peptide / Isopeptidase | ||||||
Function / homology | Hydrolases; Acting on peptide bonds (peptidases) / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / serine-type peptidase activity / Alpha/Beta hydrolase fold / proteolysis / cytoplasm / Lasso peptide isopeptidase AtxE2 Function and homology information | ||||||
Biological species | Asticcacaulis excentricus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å | ||||||
Authors | Chekan, J.R. / Nair, S.K. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2016 Title: Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates. Authors: Chekan, J.R. / Koos, J.D. / Zong, C. / Maksimov, M.O. / Link, A.J. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5txc.cif.gz | 273.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5txc.ent.gz | 227.2 KB | Display | PDB format |
PDBx/mmJSON format | 5txc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/5txc ftp://data.pdbj.org/pub/pdb/validation_reports/tx/5txc | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 78699.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48) (bacteria) Strain: ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48 / Gene: Astex_2444 / Production host: Escherichia coli (E. coli) References: UniProt: E8RUP5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 21% PEG3350, 0.4 M sodium chloride, 0.1 M Bis-Tris, pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2014 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 64978 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rsym value: 0.138 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 4.3 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→49.716 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.55
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.401→49.716 Å
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Refine LS restraints |
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LS refinement shell |
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