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Yorodumi- PDB-2dor: DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS COMPLEXED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dor | ||||||
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Title | DIHYDROOROTATE DEHYDROGENASE A FROM LACTOCOCCUS LACTIS COMPLEXED WITH OROTATE | ||||||
Components | DIHYDROOROTATE DEHYDROGENASE A | ||||||
Keywords | OXIDOREDUCTASE / PYRIMIDINE NUCLEOTIDE BIOSYNTHESIS | ||||||
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 / DIFFERENCE MAP / Resolution: 2 Å | ||||||
Authors | Rowland, P. / Larsen, S. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dor.cif.gz | 138.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dor.ent.gz | 108.3 KB | Display | PDB format |
PDBx/mmJSON format | 2dor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/2dor ftp://data.pdbj.org/pub/pdb/validation_reports/do/2dor | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8728, 0.0049, 0.4881), Vector: |
-Components
#1: Protein | Mass: 34242.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) 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: 2.81 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLISED FROM A SOLUTION CONTAINING 30% PEG 6000, 0.2M SODIUM ACETATE AND 0.1M TRIS-HCL, PH 8.5. | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 50309 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 24.2 Å2 / Rsym value: 0.061 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.25 / % possible all: 90.5 |
Reflection | *PLUS Num. measured all: 179226 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 90.5 % / Rmerge(I) obs: 0.25 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE MAP / Resolution: 2→25 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: FREE R
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Displacement parameters | Biso mean: 27.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.03 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 50283 / Num. reflection obs: 48238 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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