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Yorodumi- PDB-5euv: Crystal structure of a cold-adapted dimeric beta-D-galactosidase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5euv | ||||||
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Title | Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain | ||||||
Components | Beta-D-galactosidase | ||||||
Keywords | HYDROLASE / beta-D-galactosidase / dimeric / cold-adapted / enzyme / glycosyl hydrolase / native | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Paracoccus sp. 32d (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Rutkiewicz-Krotewicz, M. / Bujacz, A. / Pietrzyk, A.J. / Sekula, B. / Bujacz, G. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Structural studies of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d. Authors: Rutkiewicz-Krotewicz, M. / Pietrzyk-Brzezinska, A.J. / Sekula, B. / Cieslinski, H. / Wierzbicka-Wos, A. / Kur, J. / Bujacz, A. #1: Journal: Crystals / Year: 2018 Title: In Situ Random Microseeding and Streak Seeding Used for Growth of Crystals of Cold-Adapted Beta-D-Galactosidases: Crystal Structure of BetaDG from Arthrobacter sp. 32cB Authors: Rutkiewicz-Krotewicz, M. / Pietrzyk-Brzezinska, A.J. / Wanarska, M. / Cieslinski, H. / Bujacz, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5euv.cif.gz | 577.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5euv.ent.gz | 478.7 KB | Display | PDB format |
PDBx/mmJSON format | 5euv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5euv_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 5euv_full_validation.pdf.gz | 479.7 KB | Display | |
Data in XML | 5euv_validation.xml.gz | 58.2 KB | Display | |
Data in CIF | 5euv_validation.cif.gz | 86.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5euv ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5euv | HTTPS FTP |
-Related structure data
Related structure data | 5ldrC 3gm8S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 81844.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus sp. 32d (bacteria) / Plasmid: pBAD-Myc-His A / Production host: Escherichia coli (E. coli) / Strain (production host): LMD194 / References: UniProt: D1LZK0 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-BTB / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.65 % / Description: rectangular prism |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 24% PEG MME 2000, 0.1M ammonium acetate, Bis-Tris pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2013 |
Radiation | Monochromator: SI (111), mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.967 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 65993 / Num. obs: 65576 / % possible obs: 99.4 % / Redundancy: 4.39 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.67 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.94 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.07 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GM8 Resolution: 2.4→45.77 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.922 / SU B: 18.533 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.872 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→45.77 Å
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Refine LS restraints |
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