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Yorodumi- PDB-8b3y: Native Thermogutta terrifontis endoglucanase catalytic domain wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8b3y | |||||||||
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Title | Native Thermogutta terrifontis endoglucanase catalytic domain with a linker at C-terminal from glycoside hydrolase family 5 (TtEnd5A-CDC) | |||||||||
Components | Endoglucanase | |||||||||
Keywords | HYDROLASE / endoglucanase / cellulase | |||||||||
Function / homology | Function and homology information glucan catabolic process / cellulase / cellulase activity / beta-glucosidase activity / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | Thermogutta terrifontis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Hussain, N. / Naismith, J.H. / Mikolajek, H. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: To Be Published Title: Native Thermogutta terrifontis endoglucanase catalytic domain and linker at C-terminal from glycoside hydrolase family 5 (TtEnd5A-CDC) Authors: Hussain, N. / Naismith, J.H. / Mikolajek, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b3y.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b3y.ent.gz | 124.6 KB | Display | PDB format |
PDBx/mmJSON format | 8b3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b3y_validation.pdf.gz | 431.9 KB | Display | wwPDB validaton report |
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Full document | 8b3y_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 8b3y_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 8b3y_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/8b3y ftp://data.pdbj.org/pub/pdb/validation_reports/b3/8b3y | HTTPS FTP |
-Related structure data
Related structure data | 8ag9S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38603.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Initially full length gene was commercially synthesized and then was engineered in the lab to get this truncated mutant Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Gene: THTE_1171 / Plasmid: TtEnd_CDC_pEHISTEV Details (production host): pEHISTEV expression vector with inserted gene Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: A0A286RCT9, cellulase | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Well number B2 conditions of LMB screen: 1.9M Ammonium Sulphate, 0.1M MES pH 6.5 + Additive Screen (well number C11 conditions of Grid Screen Salt HR2-248: 2.9 M Sodium malonate pH 5.0) ...Details: Well number B2 conditions of LMB screen: 1.9M Ammonium Sulphate, 0.1M MES pH 6.5 + Additive Screen (well number C11 conditions of Grid Screen Salt HR2-248: 2.9 M Sodium malonate pH 5.0) TtEnd5A CD-C variant = 10.6 mg/ml. 10x Cellobiose (100 uM) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→48.26 Å / Num. obs: 93566 / % possible obs: 99 % / Redundancy: 12 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.076 / Num. unique obs: 6204 / CC1/2: 0.348 / Rpim(I) all: 0.952 / Rrim(I) all: 2.183 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8AG9 Resolution: 1.25→48.26 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.459 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.33 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→48.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.282 Å / Total num. of bins used: 20
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