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Yorodumi- PDB-1pz2: Crystal structure of a transient covalent reaction intermediate o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pz2 | |||||||||
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Title | Crystal structure of a transient covalent reaction intermediate of a family 51 alpha-L-arabinofuranosidase | |||||||||
Components | Alpha-L-arabinofuranosidase | |||||||||
Keywords | HYDROLASE / beta-alpha8-barrel | |||||||||
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 | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hoevel, K. / Shallom, D. / Niefind, K. / Belakhov, V. / Shoham, G. / Baasov, T. / Shoham, Y. / Schomburg, D. | |||||||||
Citation | Journal: Embo J. / Year: 2003 Title: Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase Authors: Hoevel, K. / Shallom, D. / Niefind, K. / Belakhov, V. / Shoham, G. / Baasov, T. / Shoham, Y. / Schomburg, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pz2.cif.gz | 217.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pz2.ent.gz | 180.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/1pz2 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/1pz2 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis |
-Components
#1: Protein | Mass: 57226.863 Da / Num. of mol.: 2 / Mutation: E175A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: T-6 / Gene: ABFA / Production host: Escherichia coli (E. coli) References: UniProt: Q9XBQ3, non-reducing end alpha-L-arabinofuranosidase #2: Sugar | #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: 2.71 Å3/Da / Density % sol: 54.64 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 18 % PEG 3350, 0.2 M NH4F, 100 mM Tris/HCl, 5% 2-Propanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 2002 |
Radiation | Monochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 169221 / Num. obs: 157884 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 96.2 |
Reflection | *PLUS Num. obs: 75814 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 96.2 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints | *PLUS
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