+Open data
-Basic information
Entry | Database: PDB / ID: 6o04 | ||||||
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Title | M.tb MenD IntII bound with Inhibitor | ||||||
Components | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | ||||||
Keywords | transferase/transferase inhibitor / menaquinone biosynthesis / ThDP dependent / decarboxylation / C-C bond ligation / Inhibitor complex / SEPHCHC synthase / transferase-transferase inhibitor complex | ||||||
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: 2.5 Å | ||||||
Authors | Johnston, J.M. / Bashiri, G. / Bulloch, E.M. / Jirgis, E.M.N. / Nigon, L.V. / Chuang, H. / Baker, E.N. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Allosteric regulation of menaquinone (vitamin K2) biosynthesis in the human pathogenMycobacterium tuberculosis. Authors: Bashiri, G. / Nigon, L.V. / Jirgis, E.N.M. / Ho, N.A.T. / Stanborough, T. / Dawes, S.S. / Baker, E.N. / Bulloch, E.M.M. / Johnston, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o04.cif.gz | 411.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o04.ent.gz | 327.9 KB | Display | PDB format |
PDBx/mmJSON format | 6o04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/6o04 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/6o04 | HTTPS FTP |
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-Related structure data
Related structure data | 6o0gC 6o0jC 6o0nC 5esuS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 4 molecules ADBC
#1: Protein | Mass: 60068.945 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: menD, Rv0555 Production host: Mycobacterium smegmatis str. MC2 155 (bacteria) References: UniProt: P9WK11, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase |
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-Non-polymers , 7 types, 432 molecules
#2: Chemical | ChemComp-DNA / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / | #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: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES/MOPS, PEK 4K, CA mix, glycerol |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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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: Dec 12, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.5→48.46 Å / Num. obs: 87576 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.361 / Rpim(I) all: 0.117 / Rrim(I) all: 0.38 / Net I/σ(I): 7.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ESU Resolution: 2.5→48.401 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.9
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105 Å2 / Biso mean: 47.7631 Å2 / Biso min: 19.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→48.401 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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