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Yorodumi- PDB-8fa5: Crystal structure of Xanthomonas campestris GH35 beta-galactosidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fa5 | ||||||
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Title | Crystal structure of Xanthomonas campestris GH35 beta-galactosidase | ||||||
Components | Beta-galactosidase | ||||||
Keywords | HYDROLASE / beta-galactosidase / xanthomonas | ||||||
Function / homology | Function and homology information beta-galactosidase / vacuole / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Godoy, A.S. / Polikarpov, I. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Xanthomonas campestris GanA beta-galactosidase Authors: Godoy, A.S. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fa5.cif.gz | 493.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fa5.ent.gz | 402.6 KB | Display | PDB format |
PDBx/mmJSON format | 8fa5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fa5_validation.pdf.gz | 449 KB | Display | wwPDB validaton report |
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Full document | 8fa5_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 8fa5_validation.xml.gz | 55.4 KB | Display | |
Data in CIF | 8fa5_validation.cif.gz | 85 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/8fa5 ftp://data.pdbj.org/pub/pdb/validation_reports/fa/8fa5 | HTTPS FTP |
-Related structure data
Related structure data | 8fa4C 8faaC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 65847.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria) Gene: bga / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P6S0 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | 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: 2.58 Å3/Da / Density % sol: 52.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2M lithium chloride, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→42.8 Å / Num. obs: 283540 / % possible obs: 97.6 % / Redundancy: 4.3 % / CC1/2: 0.99 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.7→1.75 Å / Num. unique obs: 27563 / CC1/2: 0.61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→42.793 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→42.793 Å
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Refine LS restraints |
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LS refinement shell |
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