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- PDB-7u6u: Structure of an intellectual disability-associated ornithine deca... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7u6u | ||||||||||||
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Title | Structure of an intellectual disability-associated ornithine decarboxylase variant G84R in complex with PLP | ||||||||||||
![]() | Ornithine decarboxylase | ||||||||||||
![]() | HYDROLASE / ornithine decarboxylase / intellectual disability-associated variant | ||||||||||||
Function / homology | ![]() 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 | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Zhou, X.E. / Schultz, C.R. / Powell, K.S. / Henrickson, A. / Lamp, J. / Brunzelle, J.S. / Demeler, B. / Vega, I.E. / Bachmann, A.S. / Melcher, K. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structure and Enzymatic Activity of an Intellectual Disability-Associated Ornithine Decarboxylase Variant, G84R. Authors: Zhou, X.E. / Schultz, C.R. / Suino Powell, K. / Henrickson, A. / Lamp, J. / Brunzelle, J.S. / Demeler, B. / Vega, I.E. / Bachmann, A.S. / Melcher, K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.7 KB | Display | ![]() |
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PDB format | ![]() | 141.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.7 KB | Display | ![]() |
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Full document | ![]() | 458.4 KB | Display | |
Data in XML | ![]() | 34.6 KB | Display | |
Data in CIF | ![]() | 50.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u6pC ![]() 7s3fS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47341.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: G84R variant / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium acetate trihydrate pH 7.0, 20% w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 84340 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.996 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Num. unique obs: 4377 / CC1/2: 0.62 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7S3F Resolution: 1.85→43.049 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.32 Å2 / Biso mean: 28.1147 Å2 / Biso min: 9.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.85→43.049 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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