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Yorodumi- PDB-6hfz: Crystal structure of a two-domain esterase (CEX) active on acetyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hfz | ||||||||||||
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Title | Crystal structure of a two-domain esterase (CEX) active on acetylated mannans | ||||||||||||
Components | GDSL-like protein | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / Esterase / carbohydrate / galactoglucomannan / deacetylation / biomass / gut flora | ||||||||||||
Function / homology | SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / ACETATE ION / GDSL-like protein Function and homology information | ||||||||||||
Biological species | Roseburia intestinalis L1-82 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å | ||||||||||||
Authors | Michalak, L. / La Rosa, S.L. / Rohr, A.K. / Aachmann, F.L. / Westereng, B. | ||||||||||||
Funding support | 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: A pair of esterases from a commensal gut bacterium remove acetylations from all positions on complex beta-mannans. Authors: Michalak, L. / La Rosa, S.L. / Leivers, S. / Lindstad, L.J. / Rohr, A.K. / Lillelund Aachmann, F. / Westereng, B. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hfz.cif.gz | 308.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hfz.ent.gz | 259.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hfz_validation.pdf.gz | 481.4 KB | Display | wwPDB validaton report |
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Full document | 6hfz_full_validation.pdf.gz | 494.1 KB | Display | |
Data in XML | 6hfz_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 6hfz_validation.cif.gz | 87.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/6hfz ftp://data.pdbj.org/pub/pdb/validation_reports/hf/6hfz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 42635.738 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Parts of this monomer is not well defined in the electron density map. Source: (gene. exp.) Roseburia intestinalis L1-82 (bacteria) Gene: ROSINTL182_05471 / Plasmid: pNIC-CH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7G6F8 #2: Chemical | #3: Chemical | #4: 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: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M ammonium acetate, 0.1M HEPES pH 7.5 and 25% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97531 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97531 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→48.19 Å / Num. obs: 155949 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7703 / CC1/2: 0.815 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.75→47.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.939 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.12 / 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: 35.076 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→47.87 Å
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Refine LS restraints |
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