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Yorodumi- PDB-8h2k: Cellodextrin phosphorylase from Clostridium thermocellum mutant -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h2k | |||||||||
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Title | Cellodextrin phosphorylase from Clostridium thermocellum mutant - all cysteine residues were substituted with serines | |||||||||
Components | Cellodextrin phosphorylase | |||||||||
Keywords | CARBOHYDRATE / Cellulose / Cellodextrin / Synthesis / Phosphorolysis | |||||||||
Function / homology | Function and homology information transferase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Acetivibrio thermocellus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Kuga, T. / Sunagawa, N. / Igarashi, K. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: To Be Published Title: 11 cysteine-to-serine mutations improve stability of cellodextrin phosphorylase from Clostridium thermocellum Authors: Kuga, T. / Sunagawa, N. / Igarashi, K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h2k.cif.gz | 963.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h2k.ent.gz | 638 KB | Display | PDB format |
PDBx/mmJSON format | 8h2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/8h2k ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h2k | HTTPS FTP |
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-Related structure data
Related structure data | 8h2vC 8h2wC C: citing same article (ref.) |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 112736.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acetivibrio thermocellus (bacteria) / Gene: cdp-ym4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q93HT8 |
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-Non-polymers , 5 types, 2540 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10 mg/ml protein solution was mixed 1:1 with an optimized solution consisting of 100 mM pH 5.0 sodium acetate, 12% PEG4000, and 5% glycerol with streak seeding |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 10, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→43.76 Å / Num. obs: 418204 / % possible obs: 93.49 % / Redundancy: 3.4 % / Biso Wilson estimate: 16.26 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.05459 / Rpim(I) all: 0.03548 / Net I/σ(I): 12.99 |
Reflection shell | Resolution: 1.37→1.419 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.037 / Mean I/σ(I) obs: 1.21 / Num. unique obs: 41686 / CC1/2: 0.558 / CC star: 0.846 / Rpim(I) all: 0.611 / % possible all: 93.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→43.76 Å / SU ML: 0.1846 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.5015 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.37→43.76 Å
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Refine LS restraints |
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LS refinement shell |
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