+Open data
-Basic information
Entry | Database: PDB / ID: 1f76 | ||||||
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Title | ESCHERICHIA COLI DIHYDROOROTATE DEHYDROGENASE | ||||||
Components | Dihydroorotate dehydrogenase (quinone)Dihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE / MONOMER / ALPHA-BETA-BARREL / FMN BINDING DOMAIN / OROTATE COMPLEX | ||||||
Function / homology | Function and homology information pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / FMN binding / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Norager, S. / Jensen, K.F. / Bjornberg, O. / Larsen, S. | ||||||
Citation | Journal: Structure / Year: 2002 Title: E. coli Dihydroorotate Dehydrogenase Reveals Structural and Functional Distinction between different classes of dihydroorotate dehydrogenases Authors: Norager, S. / Jensen, K.F. / Bjornberg, O. / Larsen, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary X-ray Studies of Membrane-associated Escherichia coli Dihydroorotate Dehydrogenase. Authors: Rowland, P. / Norager, S. / Jensen, K.F. / Larsen, S. #2: Journal: Biochemistry / Year: 1999 Title: The Activity of Escherichia coli Dihydroorotate Dehydrogenase is Dependent on a Conserved Loop Identified by Sequence Homology, Mutagenesis and Limited Proteolysis. Authors: Bjornberg, O. / Gruner, A.-C. / Roepstorff, P. / Jensen, K.F. #3: Journal: Flavins and Flavoproteins,Proc.13th Int.Symp. / Year: 1999 Title: The Dihydroorotate Dehydrogenases of Escherichia coli and Lactococcus Lactis Represent Two Distinct Families of the Enzyme. Authors: Bjornberg, O. / Jensen, K.F. / Gruner, A.-C. / Ottosen, M. / Sorensen, P. / Rowland, P. / Norager, S. / Larsen, S. #4: Journal: Flavins and Flavoproteins,Proc.13th Int.Symp. / Year: 1999 Title: Reduction Reactions of Two Dihydroorotate Dehydrogenases. Authors: Palfey, B. / Bjornberg, O. / 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 | 1f76.cif.gz | 290.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f76.ent.gz | 244 KB | Display | PDB format |
PDBx/mmJSON format | 1f76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/1f76 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/1f76 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a monomer. The Biological Assembly is a Monomer. |
-Components
#1: Protein | Mass: 37146.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pyrD, b0945, JW0928 / Plasmid: PAG1 / Production host: Escherichia coli (E. coli) References: UniProt: P0A7E1, dihydroorotate dehydrogenase (quinone) #2: Chemical | ChemComp-FMN / #3: Chemical | #4: Chemical | ChemComp-FMT / #5: 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: 3.57 Å3/Da / Density % sol: 65.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 3.3 to 3.7 M Na-formate, 0.1 M Na-acetate, 25 mM b-OG, 12-15 mg/ml protein, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 25, 1999 |
Radiation | Protocol: MULTIPLE ANOMALOUS DIFFRACTION / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 75583 / Num. obs: 920967 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.334 / Num. unique all: 3137 / % possible all: 84.6 |
Reflection | *PLUS Num. obs: 75583 / % possible obs: 98 % / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 84.6 % / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Structure Solved from a MAD Data Set Collected on the Se-methionine Substituted Enzyme
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1302 Å2 / ksol: 0.336959 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Refinement | *PLUS Rfactor Rfree: 0.217 / Rfactor Rwork: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.271 / Rfactor Rwork: 0.219 |