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- PDB-1j79: Molecular Structure of Dihydroorotase: A Paradigm for Catalysis T... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j79 | ||||||
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Title | Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center | ||||||
![]() | dihydroorotase | ||||||
![]() | HYDROLASE / TIM barrel / metalloenzyme / pyrimidine biosynthesis | ||||||
Function / homology | ![]() dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein homodimerization activity / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thoden, J.B. / Phillips Jr., G.N. / Neal, T.M. / Raushel, F.M. / Holden, H.M. | ||||||
![]() | ![]() Title: Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Authors: Thoden, J.B. / Phillips Jr., G.N. / Neal, T.M. / Raushel, F.M. / Holden, H.M. | ||||||
History |
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Remark 999 | SEQUENCE Based on analysis of electron density, G69 has been modeled as a proline, I119 has been ...SEQUENCE Based on analysis of electron density, G69 has been modeled as a proline, I119 has been modeled as a valine, and N243 has been modeled as a glutamine. K102 is carboxylated. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 162.7 KB | Display | ![]() |
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PDB format | ![]() | 133.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | The biological assembly is a dimer composed of chains A & B which as deposited represent the actual dimer |
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Components
#1: Protein | Mass: 38825.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ORO / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: macroseeding / batch / pH: 6 Details: PEG 3400, 2-(N-morpholino)ethanesulfonic acid (MES), potassium chloride, magnesium chloride, N-carbamoyl-DL-aspartate, pH 6.0, macroseeding / batch, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: batch method / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 7, 2000 | |||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→99 Å / Num. all: 114211 / Num. obs: 114211 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 41.1 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.3 / Num. unique all: 10107 / % possible all: 87.5 | |||||||||||||||
Reflection | *PLUS | |||||||||||||||
Reflection shell | *PLUS % possible obs: 87.5 % / Num. unique obs: 10107 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Residue 317 of chain A has no density after the CB.
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.193 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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