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- PDB-6ywu: Human OMPD-domain of UMPS (K314AcK) in complex with UMP at 1.1 An... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ywu | ||||||
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Title | Human OMPD-domain of UMPS (K314AcK) in complex with UMP at 1.1 Angstroms resolution | ||||||
![]() | Uridine 5'-monophosphate synthase | ||||||
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Function / homology | ![]() UMP biosynthetic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Tittmann, K. / Rindfleisch, S. / Krull, M. | ||||||
![]() | ![]() 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 | ![]() | 139.9 KB | Display | ![]() |
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PDB format | ![]() | 107.5 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 ![]() 6zwyC ![]() 6zwzC ![]() 6zx0C ![]() 6zx1C ![]() 6zx2C ![]() 6zx3C ![]() 7am9C ![]() 7asqC ![]() 7oqfC ![]() 7oqiC ![]() 7oqkC ![]() 7oqmC ![]() 7oqnC ![]() 7otuC ![]() 7ouzC ![]() 7ov0C ![]() 7q1hC ![]() 2qcdS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28372.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Cysteine modification on position 304 UAG stop-codon mediated introduction of acetylated lysine residue (AcK314) Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P11172, ![]() ![]() |
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#2: Chemical | ChemComp-U5P / ![]() |
#3: Chemical | ChemComp-GOL / ![]() |
#4: Chemical | ChemComp-SO4 / ![]() |
#5: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.96 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystallization: 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM ...Details: Crystallization: 100 mM Tris/HCl pH 7.8, 1.8 - 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12.5 mM UMP, 2 M L-proline |
-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![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.1→19.66 Å / Num. obs: 112207 / % possible obs: 99.2 % / Redundancy: 6.703 % / Biso Wilson estimate: 14.116 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.067 / Χ2: 0.866 / Net I/σ(I): 15.55 / Num. measured all: 752166 / Scaling rejects: 4319 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2QCD Resolution: 1.1→19.66 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.027 / ESU R Free: 0.028 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 58.94 Å2 / Biso mean: 13.673 Å2 / Biso min: 7.31 Å2
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Refinement step | Cycle: final / Resolution: 1.1→19.66 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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