+Open data
-Basic information
Entry | Database: PDB / ID: 8bre | ||||||
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Title | 1,6-anhydro-n-actetylmuramic acid kinase (AnmK) | ||||||
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 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 | 8bre.cif.gz | 361 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bre.ent.gz | 224.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bre_validation.pdf.gz | 439.2 KB | Display | wwPDB validaton report |
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Full document | 8bre_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 8bre_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 8bre_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/8bre ftp://data.pdbj.org/pub/pdb/validation_reports/br/8bre | HTTPS FTP |
-Related structure data
Related structure data | 8c0uC 8cp9C 8cpbC 3qbxS C: citing same article (ref.) S: Starting model for refinement |
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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 tag in N-terminal (unobserved, disordered). These five residues 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: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.67 Å3/Da / Density % sol: 54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 8% PEG 8000, 0.2M litium chloride, 0.05M magnesium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2022 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 0.979264 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→47.292 Å / Num. obs: 55214 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 1 / Net I/σ(I): 22.5 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4056 / CC1/2: 0.667 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QBX Resolution: 2→47.292 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.166 / SU B: 5.139 / SU ML: 0.085 / Average fsc free: 0.9678 / Average fsc work: 0.9789 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.03 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: 51.715 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.292 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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