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Yorodumi- PDB-6zpz: Structure of a-l-AraCS-Bound MgGH51 a-L-Arabinofuranosidase Cryst... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zpz | ||||||
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Title | Structure of a-l-AraCS-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1 | ||||||
Components | MgGH51 | ||||||
Keywords | HYDROLASE / arabinofuranosidse / glycosidase / GH51 / cyclophellitol | ||||||
Function / homology | Chem-LX5 Function and homology information | ||||||
Biological species | Meripilus giganteus (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 | 6zpz.cif.gz | 261.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zpz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6zpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zpz_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6zpz_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6zpz_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 6zpz_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zpz ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zpz | HTTPS FTP |
-Related structure data
Related structure data | 6zpsSC 6zpvC 6zpwC 6zpxC 6zpyC 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
-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 | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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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-Non-polymers , 3 types, 569 molecules
#4: Chemical | ChemComp-CL / |
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#5: Chemical | ChemComp-LX5 / [( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9119 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→58.12 Å / Num. obs: 79871 / % possible obs: 98.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 21.04 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.052 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 6.7 % / Num. unique obs: 3871 / CC1/2: 0.419 / Rpim(I) all: 0.694 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZPS Resolution: 1.71→55.654 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.963 / SU ML: 0.089 / Cross valid method: FREE R-VALUE / ESU R: 0.105 / ESU R Free: 0.106 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: 23.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→55.654 Å
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Refine LS restraints |
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LS refinement shell |
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