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- PDB-3li1: Crystal structure of the mutant I218A of orotidine 5'-monophospha... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3li1 | ||||||
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Title | Crystal structure of the mutant I218A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE / mutant I218A / 6-hydroxyuridine-5'-phosphate / Decarboxylase / Pyrimidine biosynthesis | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Fedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Gerlt, J.A. / Almo, S.C. | ||||||
![]() | ![]() Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation. Authors: Wood, B.M. / Amyes, T.L. / Fedorov, A.A. / Fedorov, E.V. / Shabila, A. / Almo, S.C. / Richard, J.P. / Gerlt, J.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 76 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3lhtC ![]() 3lhuC ![]() 3lhvC ![]() 3lhwC ![]() 3lhyC ![]() 3lhzC ![]() 3lldC ![]() 3llfC ![]() 3ltpC ![]() 3ltsC ![]() 3ltyC ![]() 3lv5C ![]() 3lv6C ![]() 3m1zC ![]() 3m41C ![]() 3m43C ![]() 3m44C ![]() 3m47C ![]() 3m5xC ![]() 3m5yC ![]() 3m5zC ![]() 3g18S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24842.617 Da / Num. of mol.: 2 / Mutation: I218A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Delta H / Gene: pyrF, MTH_129 / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.4M sodium citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2009 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→25 Å / Num. all: 85377 / Num. obs: 85377 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.054 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3G18 Resolution: 1.35→22.72 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1081617.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.432 Å2 / ksol: 0.410797 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.35→22.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.4 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
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Xplor file |
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