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- PDB-4fx8: Crystal structure of the mutant Q185A.R203A of orotidine 5'-monop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fx8 | ||||||
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Title | Crystal structure of the mutant Q185A.R203A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP | ||||||
![]() | Orotidine 5'-phosphate decarboxylase | ||||||
![]() | LYASE/LYASE INHIBITOR / tim barrel / inhibitor BMP / LYASE-LYASE INHIBITOR complex | ||||||
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. / Desai, B. / Gerlt, J.A. / Almo, S.C. | ||||||
![]() | ![]() Title: Conformational changes in orotidine 5'-monophosphate decarboxylase: a structure-based explanation for how the 5'-phosphate group activates the enzyme. Authors: Desai, B.J. / Wood, B.M. / Fedorov, A.A. / Fedorov, E.V. / Goryanova, B. / Amyes, T.L. / Richard, J.P. / Almo, S.C. / 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 | ![]() | 99.1 KB | Display | ![]() |
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PDB format | ![]() | 76.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3li0C ![]() 3p5yC ![]() 3p5zC ![]() 3p60C ![]() 3p61C ![]() 3qezC ![]() 3qf0C ![]() 3qmrC ![]() 3qmsC ![]() 3qmtC ![]() 3rluC ![]() 3rlvC ![]() 3sj3C ![]() 3v1pC ![]() 4fx6C ![]() 4fxrC ![]() 4gc4C ![]() 3ltpS S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 24741.531 Da / Num. of mol.: 2 / Mutation: Q185A.R203A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H Gene: pyrF, MTH_129 / Production host: ![]() ![]() References: UniProt: O26232, orotidine-5'-phosphate decarboxylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.0M Ammonium sulfate, pH 6.0, 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 315r / Detector: CCD / Date: Apr 20, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.941→46.774 Å / Num. all: 41820 / Num. obs: 41820 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3LTP Resolution: 1.9411→46.774 Å / SU ML: 0.44 / σ(F): 1.35 / Phase error: 18.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.619 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9411→46.774 Å
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Refine LS restraints |
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LS refinement shell |
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