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- PDB-6s88: Fumarate hydratase of Mycobacterium tuberculosis in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6s88 | ||||||
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Title | Fumarate hydratase of Mycobacterium tuberculosis in complex with formate and allosteric modulator N-(2-Methoxy-5-((1,2,4,5-tetrahydro-3H-benzo[d]azepin-3-yl)sulfonyl)phenyl)-2-(4-oxo-3,4-dihydrophthalazin-1-yl)acetamide | ||||||
![]() | Fumarate hydratase class II | ||||||
![]() | LYASE / Fumarate hydratase / Fumarase | ||||||
Function / homology | ![]() fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Whitehouse, A.J. / Libardo, M.D. / Kasbekar, M. / Brear, P. / Fischer, G. / Thomas, C.J. / Barry, C.E. / Boshoff, H.I. / Coyne, A.G. / Abell, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Targeting of Fumarate Hydratase fromMycobacterium tuberculosisUsing Allosteric Inhibitors with a Dimeric-Binding Mode. Authors: Whitehouse, A.J. / Libardo, M.D.J. / Kasbekar, M. / Brear, P.D. / Fischer, G. / Thomas, C.J. / Barry 3rd, C.E. / Boshoff, H.I.M. / Coyne, A.G. / Abell, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 377.5 KB | Display | ![]() |
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PDB format | ![]() | 304.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6s43SC ![]() 6s7kC ![]() 6s7sC ![]() 6s7uC ![]() 6s7wC ![]() 6s7zC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 50191.805 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: fum, fumC, DSI35_09545, ERS007663_02818, ERS007679_02635, ERS007688_02307, ERS007722_03256, ERS023446_00966, ERS024276_01230, ERS027646_00759, ERS027653_00188, ERS027654_00515, ERS027659_00384, ...Gene: fum, fumC, DSI35_09545, ERS007663_02818, ERS007679_02635, ERS007688_02307, ERS007722_03256, ERS023446_00966, ERS024276_01230, ERS027646_00759, ERS027653_00188, ERS027654_00515, ERS027659_00384, ERS027661_00671, ERS027666_02275, ERS124361_03161, SAMEA2682864_03539, SAMEA2683035_02636 Plasmid: pNAN / Production host: ![]() ![]() References: UniProt: A0A045IXZ8, UniProt: P9WN93*PLUS, fumarate hydratase #2: Chemical | #3: Chemical | ChemComp-FMT / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.49 % / Mosaicity: 0.18 ° |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NaCl, Tris, TCEP, PEG3350, DMSO, magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 21, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→121.72 Å / Num. obs: 246478 / % possible obs: 89.7 % / Redundancy: 5.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.058 / Rrim(I) all: 0.137 / Net I/σ(I): 8 / Num. measured all: 1357807 / Scaling rejects: 61 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6S43 Resolution: 1.59→84.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.088 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 133.5 Å2 / Biso mean: 26.516 Å2 / Biso min: 8.59 Å2
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Refinement step | Cycle: final / Resolution: 1.59→84.41 Å
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LS refinement shell | Resolution: 1.59→1.627 Å / Rfactor Rfree error: 0
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