[English] 日本語
![](img/lk-miru.gif)
- PDB-5i7a: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5i7a | ||||||
---|---|---|---|---|---|---|---|
Title | Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 1 [3-(3-(3,4-Dichlorophenyl)ureido)benzoic 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 synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schnell, R. / Maric, S. / Schneider, G. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 245.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 196 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5i6dC ![]() 5i7hC ![]() 5i7oC ![]() 5i7rC ![]() 5iw8C ![]() 5iwcC ![]() 3dkiS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34724.117 Da / Num. of mol.: 4 / 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 cleavage site for removal Production host: ![]() ![]() References: UniProt: P9WP52, UniProt: P9WP53*PLUS, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase #2: Chemical | ChemComp-68Q / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M MgCl2, 0.1M BT pH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91843 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→47.7 Å / Num. obs: 80146 / % possible obs: 97.3 % / Observed criterion σ(I): 1.9 / Redundancy: 2.9 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.08→2.12 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.9 / % possible all: 81 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3DKI Resolution: 2.08→75.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.968 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.707 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.08→75.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|