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Yorodumi- PDB-5xc4: Crystal structure of GH45 endoglucanase EG27II at pH4.0, in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xc4 | |||||||||
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Title | Crystal structure of GH45 endoglucanase EG27II at pH4.0, in complex with cellobiose | |||||||||
Components | Endo-beta-1,4-glucanase | |||||||||
Keywords | HYDROLASE / Cellulase / Glycoside Hydrolase Family 45 | |||||||||
Function / homology | RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / cellulase / cellulase activity / Beta Barrel / Mainly Beta / beta-cellobiose / Endo-beta-1,4-glucanase Function and homology information | |||||||||
Biological species | Ampullaria crossean (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | |||||||||
Authors | Nomura, T. / Mizutani, K. / Iwase, H. / Takahashi, N. / Mikami, B. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean. Authors: Nomura, T. / Iwase, H. / Saka, N. / Takahashi, N. / Mikami, B. / Mizutani, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xc4.cif.gz | 96 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xc4.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/5xc4 ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xc4 | HTTPS FTP |
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-Related structure data
Related structure data | 5xbuC 5xbxC 5xc8C 5xc9C 5xcaC 1wc2S C: citing same article (ref.) 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: 20915.051 Da / Num. of mol.: 1 / Fragment: UNP residues 17-195 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ampullaria crossean (invertebrata) / Gene: EG27II / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71 / References: UniProt: A7KMF0, cellulase | ||
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#2: Polysaccharide | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 32.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG4000, 200mM KCl, 50mM MES, 10mM Cellobiose |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→50 Å / Num. obs: 29924 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1463 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WC2 Resolution: 1.42→42.203 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→42.203 Å
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Refine LS restraints |
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LS refinement shell |
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