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Yorodumi- PDB-5o7z: Crystal Structure of R67A Mutant of alpha-L-arabinofuranosidase A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o7z | ||||||
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Title | Crystal Structure of R67A Mutant of alpha-L-arabinofuranosidase Ara51 from Clostridium thermocellum | ||||||
Components | Intracellular exo-alpha-(1->5)-L-arabinofuranosidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / arabinofuranose / thioligase | ||||||
Function / homology | Function and homology information arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.64 Å | ||||||
Authors | Lafite, P. / Daniellou, R. | ||||||
Citation | Journal: To Be Published Title: To be announced Authors: Pennec, A. / Lafite, P. / Ferrieres, V. / Daniellou, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o7z.cif.gz | 588.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o7z.ent.gz | 483.3 KB | Display | PDB format |
PDBx/mmJSON format | 5o7z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o7z_validation.pdf.gz | 491.4 KB | Display | wwPDB validaton report |
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Full document | 5o7z_full_validation.pdf.gz | 527.2 KB | Display | |
Data in XML | 5o7z_validation.xml.gz | 100.9 KB | Display | |
Data in CIF | 5o7z_validation.cif.gz | 138.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o7z ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o7z | HTTPS FTP |
-Related structure data
Related structure data | 5o80C 5o81C 5o82C 2c7fS 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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Unit cell |
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-Components
#1: Protein | Mass: 57429.969 Da / Num. of mol.: 6 / Mutation: R67A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: Cthe_2548 / Plasmid: p28LIC / Production host: Escherichia coli (E. coli) References: UniProt: A3DIH0, non-reducing end alpha-L-arabinofuranosidase #2: Chemical | ChemComp-DIO / #3: Water | ChemComp-HOH / | |
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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: 2.98 Å3/Da / Density % sol: 58.72 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1-4 dioxane, Na Cacodylate pH 6.5, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.64→48.813 Å / Num. obs: 122138 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.036 % / Biso Wilson estimate: 52.05 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.117 / Χ2: 1.027 / Net I/σ(I): 11.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2C7F Resolution: 2.64→48.813 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 24.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.36 Å2 / Biso mean: 42.52 Å2 / Biso min: 10.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.64→48.813 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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