+Open data
-Basic information
Entry | Database: PDB / ID: 8yjj | ||||||
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Title | Crystal structure of xylanase from Trichoderma longibrachiatum | ||||||
Components | Endo-1,4-beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / room temperature / xylanase / Trichoderma longibrachiatum | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Trichoderma longibrachiatum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nam, K.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: To Be Published Title: Crystal structure of xylanase from Trichoderma longibrachiatum Authors: Nam, K.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8yjj.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8yjj.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 8yjj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/8yjj ftp://data.pdbj.org/pub/pdb/validation_reports/yj/8yjj | HTTPS FTP |
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-Related structure data
Related structure data | 1xypS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20838.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoderma longibrachiatum (fungus) / References: UniProt: A0A2T4BZZ5, endo-1,4-beta-xylanase |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: MES, ammonium sulfate, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 22849 / % possible obs: 96 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 16.23 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.262 / Num. unique obs: 644 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XYP Resolution: 1.9→27.23 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.23 Å
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Refine LS restraints |
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LS refinement shell |
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