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Yorodumi- PDB-5eso: Crystal Structure of M. tuberculosis MenD with ThDP, Mg2+ and Iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eso | |||||||||
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Title | Crystal Structure of M. tuberculosis MenD with ThDP, Mg2+ and Isochorismate bound | |||||||||
Components | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | |||||||||
Keywords | TRANSFERASE / menaquinone biosynthesis / MenD / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase / thiamin-diphosphate dependent enzyme / pyruvate oxidase family | |||||||||
Function / homology | Function and homology information 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Johnston, J.M. / Jirgis, E.N.M. / Bashiri, G. / Bulloch, E.M.M. / Baker, E.N. | |||||||||
Citation | Journal: Structure / Year: 2016 Title: Structural Views along the Mycobacterium tuberculosis MenD Reaction Pathway Illuminate Key Aspects of Thiamin Diphosphate-Dependent Enzyme Mechanisms. Authors: Jirgis, E.N. / Bashiri, G. / Bulloch, E.M. / Johnston, J.M. / Baker, E.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eso.cif.gz | 423.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eso.ent.gz | 341.8 KB | Display | PDB format |
PDBx/mmJSON format | 5eso.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5eso_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5eso_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5eso_validation.xml.gz | 80.9 KB | Display | |
Data in CIF | 5eso_validation.cif.gz | 113.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/5eso ftp://data.pdbj.org/pub/pdb/validation_reports/es/5eso | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 60068.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: This protein contains an N-terminal His-tag not observed in the crystal structure. The numbering for the sequence in the PDB matches the numbering for the biological sequence (e.g. start ...Details: This protein contains an N-terminal His-tag not observed in the crystal structure. The numbering for the sequence in the PDB matches the numbering for the biological sequence (e.g. start site M in sequence = 1 and in PDB file this M also = 1). In 2/4 chains there is a Cys in position 26 which has been modified by B-mercaptoethanol in the protein buffer Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555 / Production host: Mycobacterium smegmatis (bacteria) References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase |
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-Non-polymers , 7 types, 806 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-FMT / #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 10% PEG 4K, 20% Glycerol, 0.02M CA, pH 7.5 (MORPHEUS G7) [CA= carboxylic acid mix, buffer=MOPS/HEPES-Na] |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→19.81 Å / Num. obs: 161660 / % possible obs: 99.9 % / Redundancy: 14.2 % / Biso Wilson estimate: 40.12 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 14.3 % / Rmerge(I) obs: 2.616 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.81 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.01 / Stereochemistry target values: ML
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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: 47.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→19.81 Å
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Refine LS restraints |
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LS refinement shell |
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