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- PDB-2oqe: Crystal Structure of Hansenula polymorpha amine oxidase in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oqe | ||||||
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Title | Crystal Structure of Hansenula polymorpha amine oxidase in complex with Xe to 1.6 Angstroms | ||||||
![]() | (Peroxisomal copper amine ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / protein-derived cofactor / TPQ / Xe / xenon complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johnson, B.J. / Wilmot, C.M. | ||||||
![]() | ![]() Title: Exploring molecular oxygen pathways in Hansenula polymorpha copper-containing amine oxidase Authors: Johnson, B.J. / Cohen, J. / Welford, R.W. / Pearson, A.R. / Schulten, K. / Klinman, J.P. / Wilmot, C.M. | ||||||
History |
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Remark 999 | SEQUENCE The author states that there is radiation damage at MET634 in the protein that is an ... SEQUENCE The author states that there is radiation damage at MET634 in the protein that is an oxidation clearly visible in chains A and B, but not in chains C,D,E, or F. The protein that went into the crystallization had an unmodified MET at position 634. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 860.3 KB | Display | ![]() |
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PDB format | ![]() | 705.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2oovC ![]() 1a2vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 |
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Unit cell |
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Details | The biological assembly is a dimer. The asymmetric unit contains three dimers. |
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Components
-Peroxisomal copper amine ... , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 74077.438 Da / Num. of mol.: 2 / Fragment: residues 13-672 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 74061.438 Da / Num. of mol.: 4 / Fragment: residues 13-672 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 3883 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/XE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-XE / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.94 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 8% PEG 8000, 0.3M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2005 |
Radiation | Monochromator: ROSENBAUM-ROCK HIGH- RESOLUTION DOUBLE-CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→99 Å / Num. obs: 587360 / % possible obs: 96.3 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.373 / % possible all: 72.9 |
-Phasing
Phasing MR | Rfactor: 0.328 / Cor.coef. Fo:Fc: 0.694
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1A2V Resolution: 1.6→46.68 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.484 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.079 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. An occupancy greater than 1.0 of atom O4 on residue 405 was used to correctly model a water that is at this position when the cofactor is ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. An occupancy greater than 1.0 of atom O4 on residue 405 was used to correctly model a water that is at this position when the cofactor is in the alternate conformer. This was required because refmac did not refine a 0.5 occupancy water and 0.5 occupancy O4 in an identical position correctly. This problem will exist at the O4 of residue 405 in chains C,D,E and F.
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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: 20.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→46.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20
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