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- PDB-2bsl: Crystal structure of L. lactis dihydroorotate dehydrogense A in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bsl | ||||||
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Title | Crystal structure of L. lactis dihydroorotate dehydrogense A in complex with 3,4-dihydroxybenzoate | ||||||
![]() | DIHYDROOROTATE DEHYDROGENASE A | ||||||
![]() | OXIDOREDUCTASE / NUCLEOTIDE METABOLISM / DIHYDROOROTATE DEHYDROGENASE / FMN / FLAVOPROTEIN / PYRIMIDINE BIOSYNTHESIS | ||||||
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 | ![]() ![]() | ||||||
![]() | Wolfe, A.E. / Hansen, M. / Gattis, S.G. / Hu, Y.-C. / Johansson, E. / Arent, S. / Larsen, S. / Palfey, B.A. | ||||||
![]() | ![]() Title: Interaction of Benzoate Pyrimidine Analogues with Class 1A Dihydroorotate Dehydrogenase from Lactococcus Lactis. Authors: Wolfe, A.E. / Thymark, M. / Gattis, S.G. / Fagan, R.L. / Hu, Y.-C. / Johansson, E. / Arent, S. / Larsen, S. / Palfey, B.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138 KB | Display | ![]() |
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PDB format | ![]() | 106.5 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 | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bx7C ![]() 1ovdS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.87874, 0.009773, 0.47719), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34242.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: P54321, UniProt: A2RJT9*PLUS, EC: 1.3.99.11 |
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-Non-polymers , 6 types, 172 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DHB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/DHB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-DHB / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | CATALYSIS: (S)-DIHYDROORO |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 54 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.5 Details: 17 MG/ML PROTEIN AND 2.6 MM 3, 4-DIOHB HANGING DROPS 2 MICROLITERS OF PROTEIN AND 2 MICROLITERS RESERVOIR: 30 % PEG 6000, 1 MM DTT, 0.2 M SODIUM ACETATE AND 0.1 M TRIS-HCL PH 8.5 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→25 Å / Num. obs: 32557 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.3→2.32 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.6 / % possible all: 62.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OVD Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 6.805 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.366 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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