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Yorodumi- PDB-5m0k: CRYSTAL STRUCTURE of endo-1,4-beta-xylanase from Cellulomonas fla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m0k | ||||||
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Title | CRYSTAL STRUCTURE of endo-1,4-beta-xylanase from Cellulomonas flavigena | ||||||
Components | Beta-xylanase | ||||||
Keywords | HYDROLASE / ALPHA-BETA BARREL / xylanase | ||||||
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 | Cellulomonas flavigena (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Gabdulkhakov, A. / Tishchenko, S. | ||||||
Citation | Journal: To Be Published Title: CRYSTAL STRUCTURE of endo-1,4-beta-xylanase from Cellulomonas flavigena Authors: Gabdulkhakov, A. / Tishchenko, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5m0k.cif.gz | 125.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m0k.ent.gz | 95.9 KB | Display | PDB format |
PDBx/mmJSON format | 5m0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m0k_validation.pdf.gz | 431.2 KB | Display | wwPDB validaton report |
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Full document | 5m0k_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 5m0k_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5m0k_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m0/5m0k ftp://data.pdbj.org/pub/pdb/validation_reports/m0/5m0k | HTTPS FTP |
-Related structure data
Related structure data | 1isvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38764.934 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulomonas flavigena (bacteria) / Gene: Cfla_0376 / Plasmid: pPic9m / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: D5UH90, endo-1,4-beta-xylanase #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: 2.29 Å3/Da / Density % sol: 46.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 15% PEG 4K, 50 mM Sodium Citrate, 20 mM Sodium chloride, 20 mM Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→50 Å / Num. obs: 21576 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.82 % / Net I/σ(I): 5.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ISV Resolution: 2.59→46.321 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 28.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59→46.321 Å
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Refine LS restraints |
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LS refinement shell |
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