[English] 日本語
Yorodumi- PDB-4mai: Structure of Aspergillus oryzae AA11 Lytic Polysaccharide Monooxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mai | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Aspergillus oryzae AA11 Lytic Polysaccharide Monooxygenase with Cu(I) | ||||||
Components | AA11 Lytic Polysaccharide Monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / chitin oxidation / GH61 / AA11 / chitin degradation | ||||||
Function / homology | Coagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / metal ion binding / COPPER (I) ION / Uncharacterized protein Function and homology information | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOTROPIC STRUCTURE REFINEMENT / SAD / Resolution: 1.4 Å | ||||||
Authors | Hemsworth, G.R. / Henrissat, B. / Walton, P.H. / Davies, G.J. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2014 Title: Discovery and characterization of a new family of lytic polysaccharide monooxygenases. Authors: Hemsworth, G.R. / Henrissat, B. / Davies, G.J. / Walton, P.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4mai.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4mai.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 4mai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mai_validation.pdf.gz | 428.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4mai_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 4mai_validation.xml.gz | 11 KB | Display | |
Data in CIF | 4mai_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/4mai ftp://data.pdbj.org/pub/pdb/validation_reports/ma/4mai | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23077.838 Da / Num. of mol.: 1 / Fragment: UNP residues 20-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: AO090102000501 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3) References: UniProt: Q2UA85, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-CU1 / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 6 Details: 10 mM zinc chloride, 100 mM MES, pH 6.0, 20% w/v PEG6000, crystals soaked in solution containing 2 mM copper chloride to replace zinc, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2013 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.39 Å / Num. all: 44262 / Num. obs: 44262 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.033 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2 / Num. unique all: 2093 / % possible all: 95.7 |
-Phasing
Phasing | Method: SAD |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ISOTROPIC STRUCTURE REFINEMENT Resolution: 1.4→42.63 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / WRfactor Rfree: 0.1671 / WRfactor Rwork: 0.1337 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9126 / SU B: 1.382 / SU ML: 0.025 / SU R Cruickshank DPI: 0.0632 / SU Rfree: 0.0587 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.042 / 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 max: 83.73 Å2 / Biso mean: 18.6373 Å2 / Biso min: 8.54 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→42.63 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
|