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Yorodumi- PDB-1jrb: The P56A mutant of Lactococcus lactis dihydroorotate dehydrogenase A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jrb | ||||||
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Title | The P56A mutant of Lactococcus lactis dihydroorotate dehydrogenase A | ||||||
Components | dihydroorotate dehydrogenase A | ||||||
Keywords | OXIDOREDUCTASE / Homodimer / alpha-beta barrel / flavoprotein / orotate complex / mutant enzyme | ||||||
Function / homology | Function and homology information dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Norager, S. / Arent, S. / Bjornberg, O. / Ottosen, M. / Lo Leggio, L. / Jensen, K.F. / Larsen, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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: Journal: Biochemistry / Year: 1997 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: Journal: Protein Sci. / Year: 1998 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: Journal: Structure / Year: 1997 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: Journal: Protein Sci. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jrb.cif.gz | 142.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jrb.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jrb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jrb ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jrb | HTTPS FTP |
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-Related structure data
Related structure data | 1jqvC 1jqxC 1jrcC 1jubC 1jueC 1ovdC 2dorS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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. |
-Components
#1: Protein | Mass: 34216.133 Da / Num. of mol.: 2 / Mutation: P56A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Plasmid: pUHE23 / Production host: Escherichia coli (E. coli) / Strain (production host): SO6645 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
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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: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.992 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 1999 |
Radiation | Monochromator: Si(111) single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→20 Å / Num. all: 452819 / Num. obs: 57637 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 1.93→1.97 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 6.2 / Num. unique all: 2390 / % possible all: 82.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Lactococcus lactis DHODA, PDB ID 2DOR Resolution: 1.9→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 has enabled us to identifie to MG-ions in the lactococcus lactis DHODA. These are also present in the P56A mutant but have been refined ...Details: Data obtained after the termination of this structure has enabled us to identifie to MG-ions in the lactococcus lactis DHODA. These are also present in the P56A mutant but have been refined as water molecules 11 and 23. The close contacts with water molecules are due to disorderd residues refined with low occupation.
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Displacement parameters | Biso mean: 22.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAIND | ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.934→2.025 Å
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