[English] 日本語
Yorodumi- PDB-4ev5: Crystal structure of copper amine oxidase-1 from Hansenula polymo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ev5 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of copper amine oxidase-1 from Hansenula polymorpha in complex with benzylamine | ||||||
Components | Peroxisomal primary amine oxidase | ||||||
Keywords | OXIDOREDUCTASE / peroxisome | ||||||
Function / homology | Function and homology information primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / peroxisome / copper ion binding Similarity search - Function | ||||||
Biological species | Ogataea angusta (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Klema, V.J. / Solheid, C.J. / Wilmot, C.M. | ||||||
Citation | Journal: To be Published Title: Crystal structure of copper amine oxidase-1 from Hansenula polymorpha in complex with benzylamine Authors: Klema, V.J. / Solheid, C.J. / Klinman, J.P. / Wilmot, C.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ev5.cif.gz | 1.6 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ev5.ent.gz | 1.3 MB | Display | PDB format |
PDBx/mmJSON format | 4ev5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ev5_validation.pdf.gz | 545.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ev5_full_validation.pdf.gz | 622.8 KB | Display | |
Data in XML | 4ev5_validation.xml.gz | 176.9 KB | Display | |
Data in CIF | 4ev5_validation.cif.gz | 254.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/4ev5 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/4ev5 | HTTPS FTP |
-Related structure data
Related structure data | 2oovS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 77663.633 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ogataea angusta (fungus) / Gene: AMO / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12807, primary-amine oxidase |
---|
-Non-polymers , 5 types, 3072 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-PEO / #5: Chemical | ChemComp-ABN / #6: Water | ChemComp-HOH / | |
---|
-Details
Source details | HANSENULA POLYMORPHA |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.91 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8% PEG8000, 0.22 M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2010 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 235420 / Num. obs: 232595 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 1.8 / % possible all: 97.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OOV Resolution: 2.25→48.9 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.791 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.52 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→48.9 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|