+Open data
-Basic information
Entry | Database: PDB / ID: 5xfm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of beta-arabinopyranosidase | ||||||
Components | Alpha-glucosidase | ||||||
Keywords | HYDROLASE / Arabinopyranosidase | ||||||
Function / homology | Function and homology information hydrolase activity, acting on glycosyl bonds / metabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Kato, K. / Okuyama, M. / Yao, M. | ||||||
Citation | Journal: Biochimie / Year: 2017 Title: A novel glycoside hydrolase family 97 enzyme: Bifunctional beta-l-arabinopyranosidase/ alpha-galactosidase from Bacteroides thetaiotaomicron. Authors: Kikuchi, A. / Okuyama, M. / Kato, K. / Osaki, S. / Ma, M. / Kumagai, Y. / Matsunaga, K. / Klahan, P. / Tagami, T. / Yao, M. / Kimura, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xfm.cif.gz | 526.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xfm.ent.gz | 429.1 KB | Display | PDB format |
PDBx/mmJSON format | 5xfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xfm_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5xfm_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 5xfm_validation.xml.gz | 97.3 KB | Display | |
Data in CIF | 5xfm_validation.cif.gz | 139.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/5xfm ftp://data.pdbj.org/pub/pdb/validation_reports/xf/5xfm | HTTPS FTP |
-Related structure data
Related structure data | 3a24S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 73212.656 Da / Num. of mol.: 4 / Mutation: F498L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: BJP75_03380, SAMN05216253_107151 / Plasmid: pCold I DNA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1H5YQC4, UniProt: Q8A1K0*PLUS #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 45 % (v/v) MPD, 0.2 M Lithium sulfate, 0.1 M MES-NaOH (pH 6.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: AREA DETECTOR / Date: Jul 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 125374 / % possible obs: 90 % / Redundancy: 3.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.15 / Rsym value: 0.126 / Net I/av σ(I): 6.6 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8292 / CC1/2: 0.88 / Rsym value: 0.391 / % possible all: 80.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A24 Resolution: 2.3→45.78 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.74
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|