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Yorodumi- PDB-2oo0: A structural insight into the inhibition of human and Leishmania ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oo0 | ||||||
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Title | A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 3-aminooxy-1-aminopropane | ||||||
Components | Ornithine decarboxylase | ||||||
Keywords | LYASE / beta-alpha barrel / sheet | ||||||
Function / homology | Function and homology information ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation ...ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / Regulation of ornithine decarboxylase (ODC) / regulation of protein catabolic process / kidney development / response to virus / cell population proliferation / positive regulation of cell population proliferation / protein homodimerization activity / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Dufe, V.T. / Ingner, D. / Khomutov, A.R. / Heby, O. / Persson, L. / Al-Karadaghi, S. | ||||||
Citation | Journal: Biochem.J. / Year: 2007 Title: A structural insight into the inhibition of human and Leishmania donovani ornithine decarboxylases by 1-amino-oxy-3-aminopropane. Authors: Dufe, V.T. / Ingner, D. / Heby, O. / Khomutov, A.R. / Persson, L. / Al-Karadaghi, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oo0.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oo0.ent.gz | 147.8 KB | Display | PDB format |
PDBx/mmJSON format | 2oo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oo0_validation.pdf.gz | 487.2 KB | Display | wwPDB validaton report |
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Full document | 2oo0_full_validation.pdf.gz | 497.1 KB | Display | |
Data in XML | 2oo0_validation.xml.gz | 36.4 KB | Display | |
Data in CIF | 2oo0_validation.cif.gz | 53.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/2oo0 ftp://data.pdbj.org/pub/pdb/validation_reports/oo/2oo0 | HTTPS FTP |
-Related structure data
Related structure data | 2on3C 1d7kS C: citing same article (ref.) 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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Details | The biological unit is a dimer which is made up by the two molecules in the asymmetric unit |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 52326.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: odc / Plasmid: pEXP5-NT/TOPO TA / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: P11926, ornithine decarboxylase |
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-Non-polymers , 5 types, 532 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.92 Å3/Da / Density % sol: 57.93 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG3350, 0.2 M ammonium acetate, O.1M MES, 2mM XAP, 0.3 % cadaverine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 17, 2006 |
Radiation | Monochromator: Bent germanium crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.043 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→29.45 Å / Num. obs: 92938 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % |
Reflection shell | Resolution: 1.9→1.949 Å / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D7K Resolution: 1.9→29.45 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.686 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 24.566 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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