+Open data
-Basic information
Entry | Database: PDB / ID: 5txe | ||||||
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Title | AtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound | ||||||
Components |
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Keywords | HYDROLASE / Isopeptidase / Lasso peptide / Natural Product | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases) / serine-type peptidase activity / defense response to bacterium / proteolysis / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Asticcacaulis excentricus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 | 5txe.cif.gz | 291 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5txe.ent.gz | 239.4 KB | Display | PDB format |
PDBx/mmJSON format | 5txe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tx/5txe ftp://data.pdbj.org/pub/pdb/validation_reports/tx/5txe | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 78683.836 Da / Num. of mol.: 2 / Mutation: S527A 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 #2: Protein/peptide | Mass: 2542.755 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_2447 / Production host: Escherichia coli (E. coli) / References: UniProt: E8RUP8 #3: 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: 2.61 Å3/Da / Density % sol: 52.81 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 18% PEG3350, 0.3 M ammonium citrate dibasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97853 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2016 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→29.817 Å / Num. obs: 86021 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.2→2.207 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.817 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.647 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.766 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→29.817 Å
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Refine LS restraints |
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