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Yorodumi- PDB-3kpf: X-ray structure of the mutant Lys300Met of polyamine oxidase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kpf | |||||||||
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Title | X-ray structure of the mutant Lys300Met of polyamine oxidase from Zea mays | |||||||||
Components | Polyamine oxidase | |||||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / POLYAMINE OXIDASE / Disulfide bond / FAD / Flavoprotein / Glycoprotein | |||||||||
Function / homology | Function and homology information polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / spermidine oxidase (propane-1,3-diamine-forming) activity / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / plant-type cell wall / polyamine catabolic process ...polyamine oxidase (propane-1,3-diamine-forming) / N8-acetylspermidine oxidase (propane-1,3-diamine-forming) / N1-acetylspermine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / spermidine oxidase (propane-1,3-diamine-forming) activity / spermine oxidase (propane-1,3-diamine-forming) activity / N8-acetylspermidine:oxygen oxidoreductase (propane-1,3-diamine-forming) activity / polyamine oxidase activity / spermine catabolic process / plant-type cell wall / polyamine catabolic process / apoplast / peroxisome / flavin adenine dinucleotide binding / oxidoreductase activity Similarity search - Function | |||||||||
Biological species | Zea mays (maize) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Fiorillo, A. / Ilari, A. / Tavladoraki, P. | |||||||||
Citation | Journal: To be Published Title: The crystal structure of the mutant K300M of polyamine oxidase from ZEA MAYS unveils the role of LYS300 in catalysis Authors: Fiorillo, A. / Ilari, A. / Tavladoraki, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kpf.cif.gz | 204.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kpf.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kpf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kpf_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3kpf_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3kpf_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 3kpf_validation.cif.gz | 50.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/3kpf ftp://data.pdbj.org/pub/pdb/validation_reports/kp/3kpf | HTTPS FTP |
-Related structure data
Related structure data | 3ku9C 1b37S 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 54529.344 Da / Num. of mol.: 2 / Mutation: K300M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zea mays (maize) / Gene: PAO / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X-33 References: UniProt: O64411, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor |
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-Sugars , 2 types, 2 molecules
#2: 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 |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 5 types, 177 molecules
#3: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | #7: Chemical | ChemComp-SO4 / | #8: 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: 4.82 Å3/Da / Density % sol: 74.47 % |
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Crystal grow | Temperature: 293 K / pH: 4.6 Details: 50% SATURATED AMMONIUM SULFATE SOLUTION, 0.1M SODIUM ACETATE pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
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Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2009 |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 45830 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.454 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B37 Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.883 / SU B: 9.163 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.445 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 24.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3495 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→2.98 Å / Total num. of bins used: 20
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