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- PDB-1jrc: The N67A mutant of Lactococcus lactis dihydroorotate dehydrogenase A -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jrc | ||||||
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Title | The N67A 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 | ![]() | 150.1 KB | Display | ![]() |
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PDB format | ![]() | 115.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 49.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jqvC ![]() 1jqxC ![]() 1jrbC ![]() 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
#1: Protein | Mass: 34199.145 Da / Num. of mol.: 2 / Mutation: N67A 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.82 % |
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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: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1999 |
Radiation | Monochromator: Triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8469 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→20 Å / Num. all: 433016 / Num. obs: 62505 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.84→1.87 Å / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2705 / % possible all: 87.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Lactococcus lactis DHODA, PDB ID 2DOR Resolution: 1.8→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Data obtained after the termination of this structure have allowed us to identify to MG-ions in lactococcus lactis DHODA. These are also present in N67A but have been refined as the waters ...Details: Data obtained after the termination of this structure have allowed us to identify to MG-ions in lactococcus lactis DHODA. These are also present in N67A but have been refined as the waters 33 and 82. close contacts between water molecules and amino acids are due to disorderd regions in which the residues are refined with low occupancy.
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Displacement parameters | Biso mean: 16.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.84→1.927 Å
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