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- PDB-5iw8: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5iw8 | ||||||
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Title | Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic acid] | ||||||
![]() | O-phosphoserine sulfhydrylase | ||||||
![]() | LYASE / Mycobacterium tuberculosis / Cysteine biosynthesis / sulphur metabolism / inhibitor | ||||||
Function / homology | ![]() [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase / Cysteine synthesis from O-phosphoserine / O-phosphoserine sulfhydrylase activity / cysteine biosynthetic process / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brunner, K. / Schnell, R. / Schneider, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis. Authors: Brunner, K. / Maric, S. / Reshma, R.S. / Almqvist, H. / Seashore-Ludlow, B. / Gustavsson, A.L. / Poyraz, O. / Yogeeswari, P. / Lundback, T. / Vallin, M. / Sriram, D. / Schnell, R. / Schneider, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 142.1 KB | Display | ![]() |
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PDB format | ![]() | 108.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 942.9 KB | Display | ![]() |
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Full document | ![]() | 948.4 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i6dC ![]() 5i7aC ![]() 5i7hC ![]() 5i7oC ![]() 5i7rC ![]() 5iwcC ![]() 3dkiS 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
#1: Protein | Mass: 34724.117 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Details: T2A mutation. Lys51 covalent modification with PLP Source: (gene. exp.) ![]() Gene: cysM, Rv1336, MTCY130.21 / Production host: ![]() ![]() References: UniProt: P9WP53, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.16 % / Description: rod / needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES 6 pH 20 %w/v PEG 6K 0.2 M NH4Cl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2015 / Details: Si mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→55.95 Å / Num. obs: 38565 / % possible obs: 99.5 % / Observed criterion σ(I): 1.9 / Redundancy: 5.5 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.167 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.04→2.15 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 1.9 / % possible all: 97.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DKI Resolution: 2.04→55.95 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.19 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.185 / 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: 29.623 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→55.95 Å
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Refine LS restraints |
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