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Yorodumi- PDB-8cp9: 1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with no... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cp9 | ||||||
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Title | 1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with non-hydrolyzable AMPPNP. | ||||||
Components | Anhydro-N-acetylmuramic acid kinase | ||||||
Keywords | TRANSFERASE / Anhydro-sugar kinase Phosphotransferase ATP binding | ||||||
Function / homology | Function and homology information anhydro-N-acetylmuramic acid kinase / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / response to antibiotic / ATP binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Jimenez-Faraco, E. / Hermoso, J.A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2023 Title: Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa. Authors: El-Araby, A.M. / Jimenez-Faraco, E. / Feltzer, R. / Martin-Garcia, J.M. / Karri, B.R. / Ramachandran, B. / Kim, C. / Fisher, J.F. / Hermoso, J.A. / Mobashery, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cp9.cif.gz | 367.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cp9.ent.gz | 226.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cp9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cp9_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8cp9_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8cp9_validation.xml.gz | 27.7 KB | Display | |
Data in CIF | 8cp9_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/8cp9 ftp://data.pdbj.org/pub/pdb/validation_reports/cp/8cp9 | HTTPS FTP |
-Related structure data
Related structure data | 8breC 8c0uC 8cpbC 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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Unit cell |
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-Components
#1: Protein | Mass: 39473.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: GAGAG expresion tag in N-terminal. These five aminoacids should be renumbered from -4 to 0. Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: anmK, PA0666 / Production host: Escherichia coli (E. coli) References: UniProt: Q9I5Q5, anhydro-N-acetylmuramic acid kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.62 Å3/Da / Density % sol: 54.32 % / Description: Hexagonal crystals |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, Na/K tartrate 0.2M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2022 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.2→47.024 Å / Num. obs: 41089 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 21 | ||||||||||||||||||
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 21.3 % / Rmerge(I) obs: 1.717 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3557 / CC1/2: 0.701 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.024 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.172 / SU B: 8.792 / SU ML: 0.126 / Average fsc free: 0.9577 / Average fsc work: 0.9763 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.041 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→47.024 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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