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Yorodumi- PDB-6k55: Inactivated mutant (D140A) of Hyperthermophilic GH6 cellobiohydro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k55 | |||||||||
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Title | Inactivated mutant (D140A) of Hyperthermophilic GH6 cellobiohydrolase II (HmCel6A) in complex with hexasaccharide | |||||||||
Components | Glucanase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / GH6 / thermostable | |||||||||
Function / homology | Function and homology information Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | Ardenticatenia bacterium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.883 Å | |||||||||
Authors | Baba, S. / Takeda, M. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T. | |||||||||
Citation | Journal: To Be Published Title: A hyperthermophilic cellobiohydrolase mined from a hot spring metagenomic data Authors: Takeda, M. / Baba, S. / Okuma, J. / Hirose, Y. / Nishimura, A. / Takata, M. / Oda, K. / Shibata, D. / Kondo, Y. / Kumasaka, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k55.cif.gz | 259.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k55.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 6k55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k55_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
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Full document | 6k55_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 6k55_validation.xml.gz | 44.3 KB | Display | |
Data in CIF | 6k55_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k55 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k55 | HTTPS FTP |
-Related structure data
Related structure data | 6k52SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 46854.234 Da / Num. of mol.: 3 / Mutation: D140A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ardenticatenia bacterium (bacteria) / Gene: D6802_06765 / Production host: Escherichia coli (E. coli) References: UniProt: A0A4Y1YS11*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | FIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS A INITIATING | |
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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: 4.71 Å3/Da / Density % sol: 73.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20%(w/v) PEG 1000, 0.1M sodium cacodylate (pH 6.5), 0.2M magnesium chloride, 0.5M cellohexaose (Soaking for 10 min) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.883→42.347 Å / Num. obs: 56407 / % possible obs: 96.07 % / Redundancy: 4.3 % / Biso Wilson estimate: 64.31 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.1994 / Rpim(I) all: 0.101 / Rrim(I) all: 0.2246 / Net I/σ(I): 5.66 |
Reflection shell | Resolution: 2.883→2.986 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.8245 / Mean I/σ(I) obs: 1.16 / Num. unique obs: 4695 / CC1/2: 0.529 / Rpim(I) all: 0.5236 / Rrim(I) all: 0.983 / % possible all: 80.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6K52 Resolution: 2.883→42.347 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.883→42.347 Å
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Refine LS restraints |
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LS refinement shell |
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