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Yorodumi- PDB-3mph: The structure of human diamine oxidase complexed with an inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mph | |||||||||
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Title | The structure of human diamine oxidase complexed with an inhibitor aminoguanidine | |||||||||
Components | Amiloride-sensitive amine oxidase | |||||||||
Keywords | OXIDOREDUCTASE / copper amine oxidase / CAO / topaquinone / TPQ / diamine oxidase / DAO / human / aminoguanidine | |||||||||
Function / homology | Function and homology information diamine oxidase / putrescine metabolic process / histamine oxidase activity / methylputrescine oxidase activity / propane-1,3-diamine oxidase activity / putrescine oxidase activity / diamine oxidase activity / primary amine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds ...diamine oxidase / putrescine metabolic process / histamine oxidase activity / methylputrescine oxidase activity / propane-1,3-diamine oxidase activity / putrescine oxidase activity / diamine oxidase activity / primary amine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / bicellular tight junction / quinone binding / specific granule lumen / peroxisome / heparin binding / copper ion binding / response to antibiotic / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / BY REFINEMENT / Resolution: 2.05 Å | |||||||||
Authors | McGrath, A.P. / Guss, J.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Correlation of active site metal content in human diamine oxidase with trihydroxyphenylalanine quinone cofactor biogenesis Authors: McGrath, A.P. / Caradoc-Davies, T. / Collyer, C.A. / 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 | 3mph.cif.gz | 325.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mph.ent.gz | 258.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mph_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 3mph_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 3mph_validation.xml.gz | 59.3 KB | Display | |
Data in CIF | 3mph_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/3mph ftp://data.pdbj.org/pub/pdb/validation_reports/mp/3mph | HTTPS FTP |
-Related structure data
Related structure data | 3hi7S S: Starting model for refinement |
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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: 83519.867 Da / Num. of mol.: 2 / Mutation: R21P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: Schneider 2 / Gene: ABP1 / Plasmid: pMTDAO / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P19801, diamine oxidase |
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-Sugars , 2 types, 6 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 1003 molecules
#4: Chemical | #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | REFER TO THE FOLLOWING PARTS OF UNP DATABASE P19801. NATURAL VARIANT FOR RESIDUE 645, SEQUENCE ...REFER TO THE FOLLOWING PARTS OF UNP DATABASE P19801. NATURAL VARIANT FOR RESIDUE 645, SEQUENCE CONFLICT OF EXPERIMENT |
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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: 2.57 Å3/Da / Density % sol: 52.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M bis-tris propane, 20%(w/v) PEG 3350, 0.2M sodium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 25, 2009 / Details: OSMIC MIRRORS |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.037→31.136 Å / Num. all: 106658 / Num. obs: 106658 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.135 / Rsym value: 0.135 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.03→2.14 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.6 / Num. measured all: 48133 / Num. unique all: 12408 / Rsym value: 0.49 / % possible all: 77 |
-Processing
Software |
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Refinement | Method to determine structure: BY REFINEMENT Starting model: PDB ENTRY 3HI7 Resolution: 2.05→31.13 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.19 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.894 / SU B: 3.969 / SU ML: 0.106 / SU R Cruickshank DPI: 0.187 / SU Rfree: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 50.23 Å2 / Biso mean: 14.103 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→31.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.046→2.099 Å / Total num. of bins used: 20
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