[English] 日本語
Yorodumi- PDB-5tkh: Neurospora crassa polysaccharide monooxygenase 2 ascorbate treated -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tkh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Neurospora crassa polysaccharide monooxygenase 2 ascorbate treated | |||||||||
Components | Lytic polysaccharide monooxygenase | |||||||||
Keywords | OXIDOREDUCTASE / polysaccharide monooxygenase | |||||||||
Function / homology | Function and homology information monooxygenase activity / hydrolase activity / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Neurospora crassa (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | |||||||||
Authors | O'Dell, W.B. / Meilleur, F. | |||||||||
Funding support | United States, 1items
| |||||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Authors: O'Dell, W.B. / Agarwal, P.K. / Meilleur, F. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5tkh.cif.gz | 306.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5tkh.ent.gz | 251.7 KB | Display | PDB format |
PDBx/mmJSON format | 5tkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tk/5tkh ftp://data.pdbj.org/pub/pdb/validation_reports/tk/5tkh | HTTPS FTP |
---|
-Related structure data
Related structure data | 5tkgC 5tkiC 4eirS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 23299.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G15G9.090, GE21DRAFT_7469 / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): SuperMan5 / References: UniProt: Q8WZQ2 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 4 types, 850 molecules
#3: Chemical | #4: Chemical | ChemComp-PER / | #5: Chemical | ChemComp-OXY / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.09 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→35.97 Å / Num. obs: 115272 / % possible obs: 95.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 8.36 Å2 / CC1/2: 0.94 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.115 / Rrim(I) all: 0.221 / Net I/σ(I): 5.8 / Num. measured all: 436269 / Scaling rejects: 704 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.244 / CC1/2: 0.891 / % possible all: 93.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4EIR Resolution: 1.2→31.821 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 12.86
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.69 Å2 / Biso mean: 13.6815 Å2 / Biso min: 3.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→31.821 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
|