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Yorodumi- PDB-1ep2: CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ep2 | ||||||
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Title | CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE | ||||||
Components | (DIHYDROOROTATE DEHYDROGENASE B ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Heterotetramer | ||||||
Function / homology | Function and homology information dihydroorotate dehydrogenase (NAD+) / dihydroorotate dehydrogenase (NAD+) activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / oxidoreductase activity / electron transfer activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Rowland, P. / Norager, S. / Jensen, K.F. / Larsen, S. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Authors: Rowland, P. / Norager, 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 | 1ep2.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ep2.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ep2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ep2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1ep2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1ep2_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | 1ep2_validation.cif.gz | 34.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1ep2 ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1ep2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a heterotetramer. There is a crystallographic two-fold axis through the center of the heterotetramer, passing through a small hydrophobic cavity between the two chain A molecules of the heterotetramer at approximate coordinates (47.61, 34.32, 13.52). The heterotetramer is held together by the two chain A molecules, with the two chain B molecules making few close contacts with each other. |
-Components
-DIHYDROOROTATE DEHYDROGENASE B ... , 2 types, 2 molecules AB
#1: Protein | Mass: 32977.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P54322, EC: 1.3.3.1 |
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#2: Protein | Mass: 28559.100 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: P56968, EC: 1.3.3.1 |
-Non-polymers , 5 types, 148 molecules
#3: Chemical | ChemComp-FMN / |
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#4: Chemical | ChemComp-ORO / |
#5: Chemical | ChemComp-FAD / |
#6: Chemical | ChemComp-FES / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2.4 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 Details: Rowland, P., (1997) Acta Crystallogr., Sect.D, 53, 802. | ||||||||||||||||||||||||||||||
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 RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 31, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.5 Å / Num. all: 89776 / Num. obs: 21335 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 4 % / Rmerge(I) obs: 0.497 / Num. unique all: 1107 / % possible all: 90.1 |
Reflection | *PLUS Num. measured all: 89776 |
-Processing
Software |
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Refinement | Resolution: 2.4→38.5 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→38.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 38.5 Å / % reflection Rfree: 5 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |