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- PDB-1jqx: The R57A mutant of Lactococcus lactis dihydroorotate dehydrogenase A -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jqx | ||||||
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Title | The R57A mutant of Lactococcus lactis dihydroorotate dehydrogenase A | ||||||
![]() | dihydroorotate dehydrogenase A | ||||||
![]() | OXIDOREDUCTASE / Homodimer / alpha-beta barrel / flavoprotein / orotate complex / mutant enzyme | ||||||
Function / homology | ![]() dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Norager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S. | ||||||
![]() | ![]() Title: Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function Authors: Norager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S. #1: ![]() Title: Active site of dihydroorotate dehydrogenase A from Lactococcus lactis investigated by chemical modification and mutagenesis Authors: Bjornberg, O. / Rowland, P. / Larsen, S. / Jensen, K.F. #2: ![]() Title: The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function Authors: Rowland, P. / Bjornberg, O. / Nielsen, F.S. / Jensen, K.F. / Larsen, S. #3: ![]() Title: The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis Authors: Rowland, P. / Nielsen, F.S. / Jensen, K.F. / Larsen, S. #4: ![]() Title: Purification and characterisation of dihydroorotate dehydrogenase A from Lactococcus lactis, crystallisation and preliminary X-ray diffraction studies of the enzyme Authors: Nielsen, F.S. / Rowland, P. / Larsen, S. / Jensen, K.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.6 KB | Display | ![]() |
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PDB format | ![]() | 118.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 51.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jqvC ![]() 1jrbC ![]() 1jrcC ![]() 1jubC ![]() 1jueC ![]() 1ovdC ![]() 2dorS S: Starting model for refinement C: citing same article ( |
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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 assymetric unit contains the biological homodimer. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34156.055 Da / Num. of mol.: 2 / Mutation: R57A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pUHE23 / Production host: ![]() ![]() References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.3.1 |
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-Non-polymers , 5 types, 731 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/ORO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG 6K, Na-acetate, TRIS-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 26, 2001 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→25 Å / Num. all: 679947 / Num. obs: 80319 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 6.8 / Num. unique all: 3949 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Lactococcus lactis DHODA PDB ID 2DOR Resolution: 1.7→25 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.8305 Å2 / ksol: 0.368323 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.006
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