[English] 日本語
Yorodumi- PDB-5ldr: Crystal structure of a cold-adapted dimeric beta-D-galactosidase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ldr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose | ||||||
Components | (Beta-D-galactosidase) x 2 | ||||||
Keywords | HYDROLASE / beta-D-galactosidase / cold-adapted / dimeric / complex / galactose | ||||||
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: 3.15 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ldr.cif.gz | 302 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ldr.ent.gz | 238.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ldr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldr ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldr | HTTPS FTP |
---|
-Related structure data
Related structure data | 5euvSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 81958.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus sp. 32d (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D1LZK0, beta-galactosidase |
---|---|
#2: Protein | Mass: 81844.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paracoccus sp. 32d (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D1LZK0 |
-Sugars , 2 types, 3 molecules
#3: Sugar | #4: Sugar | ChemComp-GLC / | |
---|
-Non-polymers , 4 types, 125 molecules
#5: Chemical | ChemComp-PEG / #6: Chemical | ChemComp-CL / #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.11 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 24% PEG 2000 0.2M ammonium acetate 0.1M Bis-Tris pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.017 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 13, 2013 / Details: mirrors |
Radiation | Monochromator: 111SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.017 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. obs: 29579 / % possible obs: 96.7 % / Redundancy: 3.65 % / CC1/2: 0.983 / Rmerge(I) obs: 0.176 / Net I/σ(I): 7.77 |
Reflection shell | Resolution: 3.15→3.25 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 1.63 / CC1/2: 0.643 / % possible all: 94.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EUV Resolution: 3.15→46.27 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.881 / SU B: 29.9 / SU ML: 0.475 / Cross valid method: THROUGHOUT / ESU R Free: 0.558 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 62.444 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→46.27 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|