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Yorodumi- PDB-5mrj: Crystal structure of Endo-1,4-beta-xylanase-like protein from Acr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mrj | ||||||
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Title | Crystal structure of Endo-1,4-beta-xylanase-like protein from Acremonium chrysogenum | ||||||
Components | Beta-xylanase | ||||||
Keywords | HYDROLASE / xylanase-like protein / Endo-1 / 4-beta-xylanase-like protein | ||||||
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 | Acremonium chrysogenum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Endo-1,4-beta-xylanase-like protein from Acremonium chrysogenum Authors: Gabdulkhakov, A. / Tishchenko, S. / Lisov, A. / Leontievsky, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrj.cif.gz | 131.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrj.ent.gz | 101.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrj ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrj | HTTPS FTP |
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-Related structure data
Related structure data | 1b30S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 43170.207 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acremonium chrysogenum (strain ATCC 11550 / CBS 779.69 / DSM 880 / JCM 23072 / IMI 49137) (fungus) Strain: ATCC 11550 / CBS 779.69 / DSM 880 / JCM 23072 / IMI 49137 Gene: ACRE_072080 / Plasmid: pPic9m / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: A0A086SY89, endo-1,4-beta-xylanase #2: Chemical | #3: 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: 3.37 Å3/Da / Density % sol: 63.55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 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: BESSY / Beamline: 14.1 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→50 Å / Num. obs: 25746 / % possible obs: 94.3 % / Redundancy: 3.95 % / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.64→2.8 Å / Redundancy: 3.71 % / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1b30 Resolution: 2.7→46.809 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 32.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→46.809 Å
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Refine LS restraints |
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LS refinement shell |
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