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Yorodumi- PDB-1tu5: Crystal structure of bovine plasma copper-containing amine oxidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tu5 | |||||||||
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Title | Crystal structure of bovine plasma copper-containing amine oxidase | |||||||||
Components | Copper amine oxidase, liver isozyme | |||||||||
Keywords | OXIDOREDUCTASE / Amine oxidase / quinoenzyme / TPQ | |||||||||
Function / homology | Function and homology information Phase I - Functionalization of compounds / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / early endosome / copper ion binding / response to antibiotic / Golgi apparatus ...Phase I - Functionalization of compounds / primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / early endosome / copper ion binding / response to antibiotic / Golgi apparatus / endoplasmic reticulum / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Molecular replacement, anomalous data / Resolution: 2.37 Å | |||||||||
Authors | Lunelli, M. / Di Paolo, M.L. / Biadene, M. / Calderone, V. / Scarpa, M. / Battistutta, R. / Rigo, A. / Zanotti, G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Crystal structure of amine oxidase from bovine serum. Authors: Lunelli, M. / Di Paolo, M.L. / Biadene, M. / Calderone, V. / Battistutta, R. / Scarpa, M. / Rigo, A. / Zanotti, G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Crystallization and preliminary X-ray data of amine oxidase from bovine serum Authors: Calderone, V. / Di Paolo, M.L. / Trabucco, M. / Biadene, M. / Battistutta, R. / Rigo, A. / Zanotti, G. #2: Journal: Structure / Year: 1995 Title: Crystal structure of a quinoenzyme: copper amine oxidase of Escherichia coli at 2 A resolution Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F. #3: Journal: Structure / Year: 1996 Title: Crystal structure of a eukaryotic (pea seedling) copper-containing amine oxidase at 2.2 A resolution Authors: Kumar, V. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. / Harvey, I. / McGuirl, M.A. / Wilce, M.C. / Zubak, V.M. #4: Journal: Biochemistry / Year: 2003 Title: The crystal structure of Pichia pastoris lysyl oxidase Authors: Duff, A.P. / Cohen, A.E. / Ellis, P.J. / Kuchar, J.A. / Langley, D.B. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tu5.cif.gz | 278.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tu5.ent.gz | 219.4 KB | Display | PDB format |
PDBx/mmJSON format | 1tu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tu5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1tu5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1tu5_validation.xml.gz | 54.6 KB | Display | |
Data in CIF | 1tu5_validation.cif.gz | 76.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/1tu5 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/1tu5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the dimer in the asymmetric unit |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 82951.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: plasma / References: UniProt: Q29437, EC: 1.4.3.6 |
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-Sugars , 2 types, 5 molecules
#2: Polysaccharide | #3: Sugar | |
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-Non-polymers , 4 types, 419 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Chemical | #7: 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: 2.06 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7 Details: 20% PEG 3350, 0.2M KH2PO4, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 22, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→27.85 Å / Num. obs: 49368 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 30.1 Å2 / Rsym value: 0.106 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.37→2.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4684 / Rsym value: 0.39 / % possible all: 77.3 |
-Processing
Software |
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Refinement | Method to determine structure: Molecular replacement, anomalous data Starting model: 1OAC, 1KSI, 1N9E Resolution: 2.37→25 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 830339.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.8916 Å2 / ksol: 0.388686 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.37→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.37→2.52 Å / Total num. of bins used: 6
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Xplor file |
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