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- PDB-5i7r: 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: 5i7r | ||||||
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Title | Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 2 [3-(3-([1,1'-biphenyl]-3-yl)ureido)benzoic 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 | ![]() ![]() ![]() | ||||||
![]() | Schnell, R. / Maric, S. / 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 | ![]() | 136.3 KB | Display | ![]() |
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PDB format | ![]() | 104.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 937.9 KB | Display | ![]() |
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Full document | ![]() | 943.2 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 36.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i6dC ![]() 5i7aC ![]() 5i7hC ![]() 5i7oC ![]() 5iw8C ![]() 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, Lys51 covalent modification with PLP Source method: isolated from a genetically manipulated source Details: Lys51 covalent modification with PLP / Source: (gene. exp.) ![]() ![]() Details (production host): N-terminal His6-tag, Thrombin site for tag removal Production host: ![]() ![]() References: UniProt: P9WP53, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % / Description: rod / needle |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M NH4-acetate, 0.1M BT pH 5.5, 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: 1.73→65.86 Å / Num. obs: 65578 / % possible obs: 98.3 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.73→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3dki Resolution: 1.73→65.85 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.597 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.104 / 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: 33.351 Å2
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Refinement step | Cycle: 1 / Resolution: 1.73→65.85 Å
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Refine LS restraints |
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