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- PDB-5iwc: 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: 5iwc | ||||||
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Title | Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 3 [4-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic acid] | ||||||
![]() | O-phosphoserine sulfhydrylase | ||||||
![]() | LYASE / Mycobacterium tuberculosis / Cysteine biosynthesis / sulphur metabolism / inhibitor / transferase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Schnell, R. / Maric, S. / Lindqvist, Y. / Schneider, G. | ||||||
![]() | ![]() 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 | ![]() | 127.8 KB | Display | ![]() |
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PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 905.2 KB | Display | ![]() |
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Full document | ![]() | 913.3 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i6dC ![]() 5i7aC ![]() 5i7hC ![]() 5i7oC ![]() 5i7rC ![]() 5iw8C ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 2 - 317 / Label seq-ID: 5 - 320
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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: Mutation: T2A, Lys51 covalent modification with PLP Source: (gene. exp.) ![]() Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a Details (production host): N-terminal His6-tah, Thrombin site for tag-removal Production host: ![]() ![]() References: UniProt: P9WP53, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.15 % / Description: rod / needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: 0.1M Bis-Tris pH 5.5, 0.2M NH4-acetate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2014 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→66.04 Å / Num. obs: 15620 / % possible obs: 96.9 % / Observed criterion σ(I): 2.1 / Redundancy: 5 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.1 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3dki Resolution: 2.7→65.43 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 15.982 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / 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: 57.24 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→65.43 Å
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Refine LS restraints |
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