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Yorodumi- PDB-2y73: THE NATIVE STRUCTURES OF SOLUBLE HUMAN PRIMARY AMINE OXIDASE AOC3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y73 | |||||||||
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Title | THE NATIVE STRUCTURES OF SOLUBLE HUMAN PRIMARY AMINE OXIDASE AOC3 | |||||||||
Components | MEMBRANE PRIMARY AMINE OXIDASE | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response ...primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / copper ion binding / protein heterodimerization activity / response to antibiotic / calcium ion binding / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Elovaara, H. / Kidron, H. / Parkash, V. / Nymalm, Y. / Bligt, E. / Ollikka, P. / Smith, D.J. / Pihlavisto, M. / Salmi, M. / Jalkanen, S. / Salminen, T.A. | |||||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Identification of Two Imidazole Binding Sites and Key Residues for Substrate Specificity in Human Primary Amine Oxidase Aoc3. Authors: Elovaara, H. / Kidron, H. / Parkash, V. / Nymalm, Y. / Bligt, E. / Ollikka, P. / Smith, D.J. / Pihlavisto, M. / Salmi, M. / Jalkanen, S. / Salminen, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2y73.cif.gz | 299.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2y73.ent.gz | 241.8 KB | Display | PDB format |
PDBx/mmJSON format | 2y73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2y73_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2y73_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2y73_validation.xml.gz | 60.5 KB | Display | |
Data in CIF | 2y73_validation.cif.gz | 82.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/2y73 ftp://data.pdbj.org/pub/pdb/validation_reports/y7/2y73 | HTTPS FTP |
-Related structure data
Related structure data | 2y74C 1us1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 84734.562 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: Q16853, primary-amine oxidase |
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-Sugars , 3 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / |
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-Non-polymers , 5 types, 362 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-IMD / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE |
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Crystal grow | pH: 7.4 Details: 0.7 M POTASSIUM/SODIUM TARTRATE, 100 MM IMIDAZOLE PH7.4, 200 MM NACL, 2M SODIUM FORMATE |
-Data collection
Diffraction | Mean temperature: 183 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.9059 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 9, 2006 / Details: VERTICALLY FOCUSING CYLINDRICAL MIRROR |
Radiation | Monochromator: SINGLE ASYMMETRICALLY CUT SI(111) CRYSTAL WITH HORIZONTAL DIFFRACTION PLANE Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9059 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.93 Å / Num. obs: 99745 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 11.8 % / Biso Wilson estimate: 36.03 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1US1 Resolution: 2.6→19.931 Å / SU ML: 0.32 / σ(F): 1.38 / Phase error: 20.91 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.63 Å2 / ksol: 0.327 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→19.931 Å
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Refine LS restraints |
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LS refinement shell |
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