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Yorodumi- PDB-5xca: Crystal structure of GH45 endoglucanase EG27II D137A mutant in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xca | |||||||||
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Title | Crystal structure of GH45 endoglucanase EG27II D137A mutant in complex with cellobiose | |||||||||
Components | Endo-beta-1,4-glucanase | |||||||||
Keywords | HYDROLASE / Cellulase / Glycoside Hydrolase Family 45 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Ampullaria crossean (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 | 5xca.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xca.ent.gz | 70.1 KB | Display | PDB format |
PDBx/mmJSON format | 5xca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xca_validation.pdf.gz | 689.3 KB | Display | wwPDB validaton report |
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Full document | 5xca_full_validation.pdf.gz | 689.3 KB | Display | |
Data in XML | 5xca_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5xca_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/5xca ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xca | HTTPS FTP |
-Related structure data
Related structure data | 5xbuC 5xbxC 5xc4C 5xc8C 5xc9C 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: 20871.041 Da / Num. of mol.: 1 / Fragment: UNP residues 17-195 / Mutation: D137A 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 | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose |
#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: 1.75 Å3/Da / Density % sol: 29.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% PEG4000, 200mM KCl, 50mM MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 32869 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 33.5 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 4 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WC2 Resolution: 1.35→41.51 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→41.51 Å
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Refine LS restraints |
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LS refinement shell |
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