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Yorodumi- PDB-6krl: Crystal structure of GH30 xylanase B from Talaromyces cellulolyti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6krl | |||||||||
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Title | Crystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris | |||||||||
Components | Mating factor alpha,GH30 Xylanase B | |||||||||
Keywords | HYDROLASE / Xylanase / Glucuronoxylanase | |||||||||
Function / homology | Function and homology information mating pheromone activity / mating / pheromone-dependent signal transduction involved in conjugation with cellular fusion / glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Saccharomyces uvarum (yeast) Talaromyces cellulolyticus CF-2612 (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | |||||||||
Authors | Nakamichi, Y. / Watanabe, M. / Inoue, H. | |||||||||
Citation | Journal: Febs Open Bio / Year: 2020 Title: Substrate recognition by a bifunctional GH30-7 xylanase B from Talaromyces cellulolyticus. Authors: Nakamichi, Y. / Watanabe, M. / Matsushika, A. / Inoue, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6krl.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6krl.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 6krl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kr/6krl ftp://data.pdbj.org/pub/pdb/validation_reports/kr/6krl | HTTPS FTP |
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-Related structure data
Related structure data | 6krnC 6iujS 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 A
#1: Protein | Mass: 59301.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The fusion protein of Mating factor alpha (UNP residues 1-89), linker, and GH30 Xylanase B (UNP residues 23-474). Source: (gene. exp.) Saccharomyces uvarum (yeast), (gene. exp.) Talaromyces cellulolyticus CF-2612 (fungus) Production host: Komagataella phaffii GS115 (fungus) References: UniProt: P25501, UniProt: A0A4V8H018, UniProt: A0A510NXC4*PLUS |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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 | 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 | ||
#4: Polysaccharide | #5: Sugar | ChemComp-NAG / | |
-Non-polymers , 2 types, 411 molecules
#6: Chemical | ChemComp-GOL / |
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#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | N |
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Sequence details | The sequence region is from a commercial vector pPIC9K (Thermo fisher scientific). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, HEPES, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.601→43.144 Å / Num. obs: 78001 / % possible obs: 99.59 % / Redundancy: 6.7 % / Biso Wilson estimate: 21.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.09292 / Rpim(I) all: 0.03888 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.601→1.658 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8014 / Mean I/σ(I) obs: 2 / Num. unique obs: 7458 / CC1/2: 0.66 / Rpim(I) all: 0.3322 / % possible all: 96.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IUJ Resolution: 1.601→43.14 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.502 / SU ML: 0.051 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.077 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.058 Å2
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Refinement step | Cycle: LAST / Resolution: 1.601→43.14 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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