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Yorodumi- PDB-7s3g: Structure of cofactor pyridoxal 5-phosphate bound human ornithine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s3g | ||||||
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Title | Structure of cofactor pyridoxal 5-phosphate bound human ornithine decarboxylase in complex with citrate at the catalytic center | ||||||
Components | Ornithine decarboxylase | ||||||
Keywords | LYASE / pyridoxal 5-phosphate / human ornithine decarboxylase / citrate | ||||||
Function / homology | Function and homology information putrescine biosynthetic process from ornithine / ornithine decarboxylase / 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 ...putrescine biosynthetic process from ornithine / ornithine decarboxylase / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Zhou, X.E. / Suino-Powell, K. / Schultz, C.R. / Aleiwi, B. / Brunzelle, J.S. / Lamp, J. / Vega, I.E. / Ellsworth, E. / Bachmann, A.S. / Melcher, K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochem.J. / Year: 2021 Title: Structural basis of binding and inhibition of ornithine decarboxylase by 1-amino-oxy-3-aminopropane. Authors: Zhou, X.E. / Suino-Powell, K. / Schultz, C.R. / Aleiwi, B. / Brunzelle, J.S. / Lamp, J. / Vega, I.E. / Ellsworth, E. / Bachmann, A.S. / Melcher, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s3g.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s3g.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 7s3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/7s3g ftp://data.pdbj.org/pub/pdb/validation_reports/s3/7s3g | HTTPS FTP |
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-Related structure data
Related structure data | 7s3fC 2oo0S 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
#1: Protein | Mass: 47241.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ODC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P11926, ornithine decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.64 Å3/Da / Density % sol: 53.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 100 mM tri-sodium citrate pH 5.0 and 30% polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→43.2496 Å / Num. obs: 122761 / % possible obs: 100 % / Redundancy: 8.2 % / CC1/2: 0.99 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.66→1.68 Å / Num. unique obs: 3597 / CC1/2: 0.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2oo0 Resolution: 1.66→43.2496 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.68 Å2 / Biso mean: 26.8266 Å2 / Biso min: 11.73 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.66→43.2496 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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