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- PDB-1eix: STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1eix | ||||||
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Title | STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP | ||||||
![]() | OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE | ||||||
![]() | LYASE / alpha-beta-barrel / protein-inhibitor complex / homodimer | ||||||
Function / homology | ![]() nucleobase-containing small molecule interconversion / carboxy-lyase activity / orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Harris, P. / Poulsen, J.C.N. / Jensen, K.F. / Larsen, S. | ||||||
![]() | ![]() Title: Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase. Authors: Harris, P. / Poulsen, J.C.N. / Jensen, K.F. / Larsen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.5 KB | Display | ![]() |
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PDB format | ![]() | 152.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a dimer constructed from chain A and B (or C and D) which are connected by a twofold. |
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Components
#1: Protein | Mass: 26378.225 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08244, orotidine-5'-phosphate decarboxylase #2: Chemical | ChemComp-BMQ / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.07 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 8000, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 26, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9902 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 102335 / Num. obs: 29678 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.243 / Num. unique all: 4946 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 102335 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 92.4 % / Mean I/σ(I) obs: 5.2 |
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Processing
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Refinement | Resolution: 2.5→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.217 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.3 |