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Yorodumi- PDB-6ywt: Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ywt | ||||||
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Title | Human OMPD-domain of UMPS (K314AcK) in complex with 6-hydroxy-UMP at 1.05 Angstroms resolution | ||||||
Components | Uridine 5'-monophosphate synthase | ||||||
Keywords | LYASE / OMPD / BMP / UMPS / Orotidine 5'-monophosphate decarboxylase | ||||||
Function / homology | Function and homology information UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / 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 / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase / 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.05 Å | ||||||
Authors | Tittmann, K. / Rindfleisch, S. / Krull, M. | ||||||
Citation | Journal: Nat Catal / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ywt.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ywt.ent.gz | 113.9 KB | Display | PDB format |
PDBx/mmJSON format | 6ywt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/6ywt ftp://data.pdbj.org/pub/pdb/validation_reports/yw/6ywt | HTTPS FTP |
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-Related structure data
Related structure data | 6yvkC 6yvlC 6yvmC 6yvnC 6yvoC 6ywuC 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 (ref.) |
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Similar structure data |
-Links
-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 (K314AcK) Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli (E. coli) References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase | ||||
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#2: Chemical | ChemComp-BMP / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Crystallization: 100 mM Tris/HCl pH 7.8, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 5mg/mL OMPD, 12 mM BMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium ...Details: Crystallization: 100 mM Tris/HCl pH 7.8, 1.6 - 1.8 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 5mg/mL OMPD, 12 mM BMP Cryo-protection: 100 mM Tris/HCl pH 7.8, 2.0 M Ammonium sulfate, 10 mM Glutathion, 5% (v/v) Glycerol, 12 mM BMP, 2 M L-proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8266 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.05→19.7 Å / Num. obs: 130413 / % possible obs: 99.9 % / Redundancy: 6.643 % / Biso Wilson estimate: 13.253 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.067 / Χ2: 0.861 / Net I/σ(I): 14.9 / Num. measured all: 866329 / Scaling rejects: 47 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QCD Resolution: 1.05→19.7 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.022 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: 80.98 Å2 / Biso mean: 12.944 Å2 / Biso min: 5.11 Å2
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Refinement step | Cycle: final / Resolution: 1.05→19.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.05→1.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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