+Open data
-Basic information
Entry | Database: PDB / ID: 8b8e | ||||||||||||
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Title | Wild-type GH11 from Blastobotrys mokoenaii | ||||||||||||
Components | BmGH11 | ||||||||||||
Keywords | CARBOHYDRATE / endo-b-1 / 4-xylanase / xylan / b-jelly roll | ||||||||||||
Function / homology | TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION Function and homology information | ||||||||||||
Biological species | Blastobotrys mokoenaii (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||||||||
Authors | Coleman, T. / Ravn, J.L. / Larsbrink, J. | ||||||||||||
Funding support | Sweden, European Union, 3items
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Citation | Journal: Microbiol Spectr / Year: 2023 Title: Yeasts Have Evolved Divergent Enzyme Strategies To Deconstruct and Metabolize Xylan. Authors: Ravn, J.L. / Ristinmaa, A.S. / Coleman, T. / Larsbrink, J. / Geijer, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b8e.cif.gz | 358.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b8e.ent.gz | 295.1 KB | Display | PDB format |
PDBx/mmJSON format | 8b8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/8b8e ftp://data.pdbj.org/pub/pdb/validation_reports/b8/8b8e | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 24242.996 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Blastobotrys mokoenaii (fungus) / Production host: Komagataella pastoris (fungus) / References: endo-1,4-beta-xylanase |
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-Non-polymers , 8 types, 766 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-144 / | #8: Chemical | ChemComp-PO4 / | #9: 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: 298 K / Method: vapor diffusion, sitting drop Details: JCSG+ kit condition D12: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20% w/v glycerol; 32.5 mg/mL BmGH11. 3 weeks at room temperature. Temp details: Room temperature |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→80.48 Å / Num. obs: 125550 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.25 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.083 / Rrim(I) all: 0.154 / Net I/σ(I): 4.3 / Num. measured all: 412389 / Scaling rejects: 1868 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AlphaFold2 model of BmGH11 Resolution: 1.55→63.11 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.78 Å2 / Biso mean: 23.5248 Å2 / Biso min: 9.53 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→63.11 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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