[English] 日本語
Yorodumi- PDB-3wiq: Crystal structure of kojibiose phosphorylase complexed with kojibiose -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wiq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of kojibiose phosphorylase complexed with kojibiose | |||||||||
Components | Kojibiose phosphorylase | |||||||||
Keywords | TRANSFERASE / (alpha/alpha)6 barrel / Phosphorylase | |||||||||
Function / homology | Function and homology information kojibiose phosphorylase / kojibiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Caldicellulosiruptor saccharolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Okada, S. / Yamamoto, T. / Watanabe, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. / Wakagi, T. / Fushinobu, S. | |||||||||
Citation | Journal: Febs J. / Year: 2014 Title: Structural and mutational analysis of substrate recognition in kojibiose phosphorylase Authors: Okada, S. / Yamamoto, T. / Watanabe, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. / Wakagi, T. / Fushinobu, S. #1: Journal: Biosci.Biotechnol.Biochem. / Year: 2011 Title: Enzymatic properties of recombinant kojibiose phosphorylase from Caldicellulosiruptor saccharolyticus ATCC43494 Authors: Yamamoto, T. / Nishio-Kosaka, M. / Izawa, S. / Aga, H. / Nishimoto, T. / Chaen, H. / Fukuda, S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wiq.cif.gz | 167.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wiq.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wiq_validation.pdf.gz | 813.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wiq_full_validation.pdf.gz | 824.5 KB | Display | |
Data in XML | 3wiq_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 3wiq_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wi/3wiq ftp://data.pdbj.org/pub/pdb/validation_reports/wi/3wiq | HTTPS FTP |
-Related structure data
Related structure data | 3wirC 1h54S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 88685.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor saccharolyticus (bacteria) Strain: ATCC 43494 / DSM 8903 / Gene: Csac_0444 / Plasmid: pRSET0439-C-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus(DE3)-RIL / References: UniProt: A4XGP2, kojibiose phosphorylase |
---|---|
#2: Polysaccharide | alpha-D-glucopyranose-(1-2)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | ALPHA-1,2-LINKED GLC AND BGC IS KOJIBIOSE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.28 Å3/Da / Density % sol: 76.71 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 5mM kojibiose, 0.2M NaCl, 2.0M (NH4)2SO4, 0.1M Na-cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2011 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 47021 / Num. obs: 47003 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Rsym value: 0.105 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 13.9 % / Num. unique all: 2315 / Rsym value: 0.982 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H54 Resolution: 2.8→48.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.975 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.278 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.61 Å2 / Biso mean: 56.1333 Å2 / Biso min: 25.23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→48.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.795→2.868 Å / Total num. of bins used: 20
|