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Yorodumi- PDB-5yxt: Crystal structure of reducing end xylose-releasing exo-oligoxylanase -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yxt | ||||||
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Title | Crystal structure of reducing end xylose-releasing exo-oligoxylanase | ||||||
Components | Reducing end xylose-releasing exo-oligoxylanase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | Paenibacillus barengoltzii G22 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Jiang, Z.Q. / You, X. / Huang, P. / Ma, J.W. | ||||||
Citation | Journal: To Be Published Title: Structure of glycoside hydrolase family 8 xylanase at 1.88 Angstroms resolution Authors: Jiang, Z.Q. / You, X. / Huang, P. / Ma, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yxt.cif.gz | 324.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yxt.ent.gz | 262.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/5yxt ftp://data.pdbj.org/pub/pdb/validation_reports/yx/5yxt | HTTPS FTP |
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-Related structure data
Related structure data | 1wu4S S: Starting model for refinement |
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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: 44091.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus barengoltzii G22 (bacteria) Gene: C812_03928 / Production host: Escherichia coli (E. coli) / References: UniProt: R9L536 #2: Water | ChemComp-HOH / | |
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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: 39.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium thiocyanate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→22.35 Å / Num. obs: 105939 / % possible obs: 93 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 1.88→1.94 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WU4 Resolution: 1.88→22.35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 50.01 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→22.35 Å
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Refine LS restraints |
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LS refinement shell |
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