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Yorodumi- PDB-7mfn: N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphyloco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mfn | ||||||
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Title | N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphylococcus aureus (strain MRSA USA300) | ||||||
Components | N-acetylmannosamine-6-phosphate 2-epimerase | ||||||
Keywords | ISOMERASE / Epimerase / NanE | ||||||
Function / homology | Function and homology information N-acylglucosamine-6-phosphate 2-epimerase / : / N-acylglucosamine-6-phosphate 2-epimerase activity / N-acetylmannosamine metabolic process / N-acetylneuraminate catabolic process / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Currie, M.J. / Dobson, R.C.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 Title: N-acetylmannosamine-6-phosphate 2-epimerase uses a novel substrate-assisted mechanism to catalyze amino sugar epimerization. Authors: Currie, M.J. / Manjunath, L. / Horne, C.R. / Rendle, P.M. / Subramanian, R. / Friemann, R. / Fairbanks, A.J. / Muscroft-Taylor, A.C. / North, R.A. / Dobson, R.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mfn.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mfn.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7mfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mfn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7mfn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7mfn_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 7mfn_validation.cif.gz | 41 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/7mfn ftp://data.pdbj.org/pub/pdb/validation_reports/mf/7mfn | HTTPS FTP |
-Related structure data
Related structure data | 6vvaSC 7mfsC 7mqtC S: Starting model for refinement 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: 24513.037 Da / Num. of mol.: 2 / Mutation: E180A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: nanE, BTN44_01590, EP54_02960, EQ90_08785, ERS072840_01491, FA040_00085, HMPREF3211_02501, NCTC10654_00351, NCTC10702_00560, NCTC7878_00328, RK64_02155 Production host: Escherichia coli (E. coli) References: UniProt: X5EM89, N-acylglucosamine-6-phosphate 2-epimerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 3.04 Å3/Da / Density % sol: 59.57 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1 M trisodium citrate, 0.1 M sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95366 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95366 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→46.4 Å / Num. obs: 87948 / % possible obs: 99.5 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.55→1.57 Å / Num. unique obs: 8254 / CC1/2: 0.842 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VVA Resolution: 1.55→42.004 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.25 / SU ML: 0.044 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064 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: 19.856 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→42.004 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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