[English] 日本語
Yorodumi- PDB-4xwz: The crystal structure of Fructosyl amine: oxygen oxidoreductase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xwz | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of Fructosyl amine: oxygen oxidoreductase (Amadoriase I) from Aspergillus fumigatus in complex with the substrate fructosyl lysine | ||||||
Components | Fructosyl amine:oxygen oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / FAOX / FAODs / complex / substrate | ||||||
Function / homology | Function and homology information saccharopine oxidase activity / sarcosine oxidase activity / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Rigoldi, F. / Gautieri, A. / Dalle Vedove, A. / Lucarelli, A.P. / Vesentini, S. / Parisini, E. | ||||||
Citation | Journal: Proteins / Year: 2016 Title: Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate-bound complex. Authors: Rigoldi, F. / Gautieri, A. / Dalle Vedove, A. / Lucarelli, A.P. / Vesentini, S. / Parisini, E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4xwz.cif.gz | 203.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4xwz.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xwz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xwz_validation.pdf.gz | 972.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4xwz_full_validation.pdf.gz | 981 KB | Display | |
Data in XML | 4xwz_validation.xml.gz | 39.3 KB | Display | |
Data in CIF | 4xwz_validation.cif.gz | 57.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/4xwz ftp://data.pdbj.org/pub/pdb/validation_reports/xw/4xwz | HTTPS FTP |
-Related structure data
Related structure data | 4wctSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 51336.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (mold) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: O42629 #2: Chemical | #3: Chemical | #4: Sugar | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.93 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate 0.1M, 10%Peg4K, 15% 2-Propanol / PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.96 Å / Num. obs: 80799 / % possible obs: 99.3 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.736 / Mean I/σ(I) obs: 2.6 / % possible all: 93 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WCT Resolution: 1.9→47.96 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.731 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / 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: 24.802 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.9→47.96 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|