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Yorodumi- PDB-5mpv: Crystal structure of a Mycobacterium tuberculosis chorismate muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mpv | ||||||
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Title | Crystal structure of a Mycobacterium tuberculosis chorismate mutase optimized for high autonomous activity by directed evolution | ||||||
Components | Intracellular chorismate mutase | ||||||
Keywords | ISOMERASE / chorismate mutase / directed evolution / Mycobacterium tuberculosis | ||||||
Function / homology | Function and homology information aromatic amino acid family biosynthetic process, prephenate pathway / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / amino acid biosynthetic process / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Thorbjornsrud, H.V. / Kamarauskaite, J. / Kast, P. / Krengel, U. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Evolving the naturally compromised chorismate mutase from Mycobacterium tuberculosis to top performance. Authors: Fahrig-Kamarauskait, J. / Wurth-Roderer, K. / Thorbjornsrud, H.V. / Mailand, S. / Krengel, U. / Kast, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mpv.cif.gz | 30.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mpv.ent.gz | 19.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mpv_validation.pdf.gz | 415.9 KB | Display | wwPDB validaton report |
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Full document | 5mpv_full_validation.pdf.gz | 415.8 KB | Display | |
Data in XML | 5mpv_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 5mpv_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/5mpv ftp://data.pdbj.org/pub/pdb/validation_reports/mp/5mpv | HTTPS FTP |
-Related structure data
Related structure data | 2w1aS S: Starting model for refinement |
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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
#1: Protein | Mass: 10063.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv0948c, MTCY10D7.26 / Plasmid: pKTCMM / Production host: Escherichia coli (E. coli) / Variant (production host): KA13 / References: UniProt: P9WIC1, chorismate mutase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG MME 2000, 0.2 M trimehylamino-N-oxide, 0.1 M Tris. Microseeding. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953723 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953723 Å / Relative weight: 1 |
Reflection | Resolution: 1.488→47.27 Å / Num. obs: 16797 / % possible obs: 95.5 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rrim(I) all: 0.056 / Net I/σ(I): 15.01 |
Reflection shell | Resolution: 1.488→1.496 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 0.33 / CC1/2: 0.332 / Rrim(I) all: 2.806 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W1A Resolution: 1.49→47.27 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.36 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.423 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→47.27 Å
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Refine LS restraints |
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