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- PDB-1km2: crystal structure of orotidine monophosphate mutant Q185A with 6-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1km2 | ||||||
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Title | crystal structure of orotidine monophosphate mutant Q185A with 6-azaUMP | ||||||
![]() | OROTIDINE 5'-PHOSPHATE DECARBOXYLASE | ||||||
![]() | LYASE / TIM barrel | ||||||
Function / homology | ![]() orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, N. / Gillon, W. / Pai, E.F. | ||||||
![]() | ![]() Title: Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography. Authors: Wu, N. / Gillon, W. / Pai, E.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.8 KB | Display | ![]() |
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PDB format | ![]() | 42.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.6 KB | Display | ![]() |
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Full document | ![]() | 443.6 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1klyC ![]() 1klzC ![]() 1km0C ![]() 1km1C ![]() 1km3C ![]() 1km4C ![]() 1km5C ![]() 1km6C C: citing same article ( |
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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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Components on special symmetry positions |
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Details | the other half of the biological dimer is generated by the two fold axis -x, -y, z+1/2 |
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Components
#1: Protein | Mass: 26738.797 Da / Num. of mol.: 1 / Mutation: Q185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pET15b / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase |
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#2: Chemical | ChemComp-UP6 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.49 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: trisodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 / Details: Wu, N., (2000) Acta Crystallogr., Sect.D, 56, 912. | ||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2000 / Details: bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 34229 / Num. obs: 34229 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.8 Å2 |
Reflection shell | Resolution: 1.5→1.59 Å / % possible all: 94.6 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 30 Å / Num. measured all: 402681 / Rmerge(I) obs: 0.054 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.6417 Å2 / ksol: 0.39042 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→29.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 30 Å / Rfactor obs: 0.169 / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.169 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.202 / Rfactor Rwork: 0.182 |