[English] 日本語
Yorodumi- PDB-1j79: Molecular Structure of Dihydroorotase: A Paradigm for Catalysis T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j79 | ||||||
---|---|---|---|---|---|---|---|
Title | Molecular Structure of Dihydroorotase: A Paradigm for Catalysis Through the Use of a Binuclear Metal Center | ||||||
Components | dihydroorotase | ||||||
Keywords | HYDROLASE / TIM barrel / metalloenzyme / pyrimidine biosynthesis | ||||||
Function / homology | Function and homology information dihydroorotase / pyrimidine nucleotide biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / protein homodimerization activity / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Thoden, J.B. / Phillips Jr., G.N. / Neal, T.M. / Raushel, F.M. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Authors: Thoden, J.B. / Phillips Jr., G.N. / Neal, T.M. / Raushel, F.M. / Holden, H.M. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE Based on analysis of electron density, G69 has been modeled as a proline, I119 has been ...SEQUENCE Based on analysis of electron density, G69 has been modeled as a proline, I119 has been modeled as a valine, and N243 has been modeled as a glutamine. K102 is carboxylated. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j79.cif.gz | 162.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j79.ent.gz | 133.6 KB | Display | PDB format |
PDBx/mmJSON format | 1j79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/1j79 ftp://data.pdbj.org/pub/pdb/validation_reports/j7/1j79 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer composed of chains A & B which as deposited represent the actual dimer |
-Components
#1: Protein | Mass: 38825.172 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PYRC / Production host: Escherichia coli (E. coli) / References: UniProt: P05020, dihydroorotase #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ORO / | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: macroseeding / batch / pH: 6 Details: PEG 3400, 2-(N-morpholino)ethanesulfonic acid (MES), potassium chloride, magnesium chloride, N-carbamoyl-DL-aspartate, pH 6.0, macroseeding / batch, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: batch method / Details: used macroseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.14020, 1.14050, 1.09045, 1.03320 | |||||||||||||||
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 7, 2000 | |||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.5→99 Å / Num. all: 114211 / Num. obs: 114211 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 41.1 | |||||||||||||||
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.3 / Num. unique all: 10107 / % possible all: 87.5 | |||||||||||||||
Reflection | *PLUS | |||||||||||||||
Reflection shell | *PLUS % possible obs: 87.5 % / Num. unique obs: 10107 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.7→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Residue 317 of chain A has no density after the CB.
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: TNT / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor all: 0.193 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|