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- PDB-7oqn: Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7oqn | ||||||
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Title | Human OMPD-domain of UMPS in complex with substrate OMP at 1.10 Angstroms resolution, 30 minutes soaking | ||||||
![]() | (Uridine 5'-monophosphate ...) x 2 | ||||||
![]() | LYASE / OMPD / UMPS / UMP | ||||||
Function / homology | ![]() UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rindfleisch, S. / Rabe von Pappenheim, F. / Tittmann, K. | ||||||
![]() | ![]() Title: Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis Authors: Rindfleisch, S. / Krull, M. / Uranga, J. / Schmidt, T. / Rabe von Pappenheim, F. / Kirck, L.L. / Balouri, A. / Schneider, T. / Chari, A. / Kluger, R. / Bourenkov, G. / Diederichsen, U. / ...Authors: Rindfleisch, S. / Krull, M. / Uranga, J. / Schmidt, T. / Rabe von Pappenheim, F. / Kirck, L.L. / Balouri, A. / Schneider, T. / Chari, A. / Kluger, R. / Bourenkov, G. / Diederichsen, U. / Mata, R.A. / Tittmann, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 261.6 KB | Display | ![]() |
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PDB format | ![]() | 208.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yvkC ![]() 6yvlC ![]() 6yvmC ![]() 6yvnC ![]() 6yvoC ![]() 6ywtC ![]() 6ywuC ![]() 6zwySC ![]() 6zwzC ![]() 6zx0C ![]() 6zx1C ![]() 6zx2C ![]() 6zx3C ![]() 7am9C ![]() 7asqC ![]() 7oqfC ![]() 7oqiC ![]() 7oqkC ![]() 7oqmC ![]() 7otuC ![]() 7ouzC ![]() 7ov0C ![]() 7q1hC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Uridine 5'-monophosphate ... , 2 types, 2 molecules AB
#1: Protein | Mass: 28113.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase |
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#2: Protein | Mass: 28081.451 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase |
-Non-polymers , 4 types, 714 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/U.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/U.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: Ammonium sulfate, Tris/HCl, Glutathion, Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.827 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→42.54 Å / Num. obs: 220244 / % possible obs: 98.7 % / Redundancy: 3.467 % / Biso Wilson estimate: 14.499 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.05 / Χ2: 0.88 / Net I/σ(I): 15.36 / Num. measured all: 763641 / Scaling rejects: 241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ZWY Resolution: 1.1→42.54 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 1.258 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.02 Å2 / Biso mean: 16.359 Å2 / Biso min: 9.26 Å2
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Refinement step | Cycle: final / Resolution: 1.1→42.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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