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Yorodumi- PDB-6zpw: Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zpw | ||||||
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Title | Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 2 | ||||||
Components | MgGH51 | ||||||
Keywords | HYDROLASE / arabinofuranosidse / glycosidase / GH51 | ||||||
Function / homology | ACETATE ION Function and homology information | ||||||
Biological species | Meripilus giganteus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.329 Å | ||||||
Authors | McGregor, N.G.S. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structure of a GH51 alpha-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi. Authors: McGregor, N.G.S. / Turkenburg, J.P. / Morkeberg Krogh, K.B.R. / Nielsen, J.E. / Artola, M. / Stubbs, K.A. / Overkleeft, H.S. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zpw.cif.gz | 468.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zpw.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zpw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zpw ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zpw | HTTPS FTP |
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-Related structure data
Related structure data | 6zpsSC 6zpvC 6zpxC 6zpyC 6zpzC 6zq0C 6zq1C S: Starting model for refinement C: citing same article (ref.) |
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Similar 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, 1 molecules AAA
#1: Protein | Mass: 67687.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meripilus giganteus (fungus) / Production host: Aspergillus oryzae (mold) / References: non-reducing end alpha-L-arabinofuranosidase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source |
-Non-polymers , 5 types, 739 molecules
#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-CL / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 2.4 M (NH4)2SO4, 0.1 M NaOAc, pH 6, 20% glycerol PH range: 6 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.329→80.743 Å / Num. obs: 265496 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.33→1.35 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 12835 / CC1/2: 0.521 / Rpim(I) all: 0.727 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZPS Resolution: 1.329→80.743 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.146 / WRfactor Rwork: 0.124 / SU B: 1.258 / SU ML: 0.022 / Average fsc free: 0.9502 / Average fsc work: 0.9548 / Cross valid method: FREE R-VALUE / ESU R: 0.03 / ESU R Free: 0.031 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.393 Å2
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Refinement step | Cycle: LAST / Resolution: 1.329→80.743 Å
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Refine LS restraints |
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LS refinement shell |
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