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Yorodumi- PDB-6k52: Hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k52 | ||||||
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Title | Hyperthermophilic GH6 cellobiohydrolase (HmCel6A) from the microbial flora of a Japanese hot spring | ||||||
Components | GH6 cellobiohydrolase, HMCEL6A | ||||||
Keywords | HYDROLASE / glycoside hydrolase / GH6 / thermostable | ||||||
Function / homology | 1, 4-beta cellobiohydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ACETATE ION Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68000139531 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 | 6k52.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k52.ent.gz | 86.9 KB | Display | PDB format |
PDBx/mmJSON format | 6k52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k52 ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k52 | HTTPS FTP |
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-Related structure data
Related structure data | 6k55C 1oc5S 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46898.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) References: cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | Sequence details | FIRST MET IS A INITIATING METHIONINE. THIS DNA SEQUENCE HAS BEEN DEPOSITED TO DDBJ WITH A ...FIRST MET IS A INITIATING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% (W/V) PEG 1000, 0.2M CAICIUM ACETATE, 0.1M IMIDAZOLE (PH 8.0) |
-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: Oct 29, 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: 1.68→50 Å / Num. obs: 97033 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 17.3900593193 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.018 / Rrim(I) all: 0.074 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 9626 / CC1/2: 0.961 / Rpim(I) all: 0.155 / Rrim(I) all: 0.617 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OC5 Resolution: 1.68000139531→32.9103974351 Å / SU ML: 0.176042297081 / Cross valid method: FREE R-VALUE / σ(F): 1.33476296841 / Phase error: 21.1813420271
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3657637173 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68000139531→32.9103974351 Å
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Refine LS restraints |
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LS refinement shell |
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