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Yorodumi- PDB-7ax7: Crystal structure of the Xyl-CE4 domain of a multidomain xylanase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ax7 | ||||||
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Title | Crystal structure of the Xyl-CE4 domain of a multidomain xylanase from the hindgut metagenome of Trinervitermes trinervoides | ||||||
Components | Endo-1,4-beta-xylanase | ||||||
Keywords | METAL BINDING PROTEIN / Xyl-CE4 uses Co2+ to cleave acetyl groups from acetylated xylan molecules. As part of a multidomain assembly / CE4 functions independently of other domain components. | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05000181627 Å | ||||||
Authors | Anye, V. / Schubert, W.D. | ||||||
Funding support | South Africa, 1items
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Citation | Journal: Plos One / Year: 2022 Title: Structural and biophysical characterization of the multidomain xylanase Xyl. Authors: Anye, V. / Kruger, R.F. / Schubert, W.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ax7.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ax7.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ax7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/7ax7 ftp://data.pdbj.org/pub/pdb/validation_reports/ax/7ax7 | HTTPS FTP |
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-Related structure data
Related structure data | 7ay3C 7aypC 7zszC 2c71S 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
#1: Protein | Mass: 23812.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) uncultured bacterium (environmental samples) Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140HJ20, endo-1,4-beta-xylanase |
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#2: Chemical | ChemComp-CO / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.17 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 292.2 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10 mg/mL in 20 mM Tris-HCl pH 7.5, 10 mM NaCl, 8 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→23.07 Å / Num. obs: 13512 / % possible obs: 99 % / Redundancy: 2 % / Biso Wilson estimate: 13.713555817 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.019 / Net I/av σ(I): 18 / Net I/σ(I): 2.74 |
Reflection shell | Resolution: 2.05→2.12 Å / Num. unique obs: 722 / CC1/2: 0.991 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C71 Resolution: 2.05000181627→19.5413775456 Å / SU ML: 0.250769489372 / Cross valid method: FREE R-VALUE / σ(F): 1.4376150803 / Phase error: 25.4581162604 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 14.1404325504 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05000181627→19.5413775456 Å
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Refine LS restraints |
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LS refinement shell |
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