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Yorodumi- PDB-7whe: The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K) wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7whe | ||||||
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Title | The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K) with xylobiose | ||||||
Components | Beta-xylanase | ||||||
Keywords | HYDROLASE / GH10 family xylanase | ||||||
Function / homology | Function and homology information cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Aspergillus fumigatus (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Li, G.Q. / Zhang, R.F. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: The mutant crystal structure of b-1,4-Xylanase (XynAF1_R246K) with xylobiose Authors: Li, G.Q. / Zhang, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7whe.cif.gz | 145.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7whe.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 7whe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/7whe ftp://data.pdbj.org/pub/pdb/validation_reports/wh/7whe | HTTPS FTP |
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-Related structure data
Related structure data | 6jdtS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35212.184 Da / Num. of mol.: 2 / Mutation: R246K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_00377 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A229WLM4, endo-1,4-beta-xylanase #2: Polysaccharide | beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Sodium formate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97914 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→50 Å / Num. obs: 58475 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Rrim(I) all: 0.154 / Χ2: 0.995 / Net I/σ(I): 6 / Num. measured all: 764269 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JDT Resolution: 1.75→30.11 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.994 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.44 Å2 / Biso mean: 18.305 Å2 / Biso min: 10.04 Å2
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Refinement step | Cycle: final / Resolution: 1.75→30.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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