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Yorodumi- PDB-8ow9: Crystal structure of Tannerella forsythia MurNAc kinase MurK in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ow9 | |||||||||
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Title | Crystal structure of Tannerella forsythia MurNAc kinase MurK in complex with N-acetylmuramic acid (MurNAc) | |||||||||
Components | Putative novel MurNAc kinase | |||||||||
Keywords | TRANSFERASE / sugar phosphorylation | |||||||||
Function / homology | phosphorylation / ATPase, nucleotide binding domain / kinase activity / N-acetyl-beta-muramic acid / Putative novel MurNAc kinase Function and homology information | |||||||||
Biological species | Tannerella forsythia (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Stasiak, A.C. / Gogler, K. / Fink, P. / Stehle, T. / Zocher, G. | |||||||||
Funding support | European Union, Germany, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: N-acetylmuramic acid recognition by MurK kinase from the MurNAc auxotrophic oral pathogen Tannerella forsythia. Authors: Stasiak, A.C. / Gogler, K. / Borisova, M. / Fink, P. / Mayer, C. / Stehle, T. / Zocher, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ow9.cif.gz | 398.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ow9.ent.gz | 262.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ow9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ow9_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8ow9_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8ow9_validation.xml.gz | 66.3 KB | Display | |
Data in CIF | 8ow9_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/8ow9 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8ow9 | HTTPS FTP |
-Related structure data
Related structure data | 8oqkC 8oqwC 8oqxC 8ow7C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32480.295 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: murK, TFUB20_00044 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D3UBL2 #2: Sugar | ChemComp-AMU / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 15% PEG10000, 100 mM trisodium citrate pH 5.5, 2% v/v 1,4-dioxane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 30, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→49.13 Å / Num. obs: 49814 / % possible obs: 98.5 % / Redundancy: 14.1 % / CC1/2: 0.994 / Net I/σ(I): 8.06 |
Reflection shell | Resolution: 2.7→2.87 Å / Num. unique obs: 8018 / CC1/2: 0.466 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.13 Å / Cross valid method: FREE R-VALUE / σ(F): 569.45 / Phase error: 30.5926 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 68.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.13 Å
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Refine LS restraints |
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LS refinement shell |
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