+Open data
-Basic information
Entry | Database: PDB / ID: 6ne9 | ||||||
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Title | Bacteroides intestinalis acetyl xylan esterase (BACINT_01039) | ||||||
Components | Isoamylase protein | ||||||
Keywords | HYDROLASE / carbohydrate esterase family 1 | ||||||
Function / homology | Esterase-like / Putative esterase / Immunoglobulin E-set / Alpha/Beta hydrolase fold / Immunoglobulin-like fold / DI(HYDROXYETHYL)ETHER / Putative esterase Function and homology information | ||||||
Biological species | Bacteroides intestinalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.738 Å | ||||||
Authors | Koropatkin, N.M. / Pereira, G.V. / Cann, I. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Degradation of complex arabinoxylans by human colonic Bacteroidetes Authors: Pereira, G.V. / DAlessandro-Gabazza, C. / Farris, J. / Wefers, D. / Mackie, R. / Koropatkin, N.M. / Gabazza, E.C. / Cann, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ne9.cif.gz | 278.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ne9.ent.gz | 240.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ne9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/6ne9 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/6ne9 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43453.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides intestinalis (bacteria) / Gene: HMPREF2531_02003 / Production host: Escherichia coli (E. coli) / References: UniProt: B3C975*PLUS |
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-Non-polymers , 5 types, 509 molecules
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-CL / | #6: 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: 2.54 Å3/Da / Density % sol: 51.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10 mM Ammonium sulfate, 80 mM Sodium Cacodylate pH 6.5, and 21% PEG4000 Temp details: room temp |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.738→28.6 Å / Num. obs: 145030 / % possible obs: 91.71 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.738→1.8 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.2286 / Num. unique obs: 2851 / % possible all: 28.61 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.738→28.598 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.93 Å2 / Biso mean: 26.2957 Å2 / Biso min: 7.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.738→28.598 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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