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Yorodumi- PDB-5i6d: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5i6d | ||||||
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Title | Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 5 [3-(3-(p-Tolyl)ureido) benzoic acid] | ||||||
Components | O-phosphoserine sulfhydrylase | ||||||
Keywords | LYASE / Cysteine synthase / Mycobacterium tuberculosis / inhibitor / transferase | ||||||
Function / homology | Function and homology information [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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Schnell, R. / Maric, S. / Schneider, G. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Med.Chem. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5i6d.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i6d.ent.gz | 202.5 KB | Display | PDB format |
PDBx/mmJSON format | 5i6d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/5i6d ftp://data.pdbj.org/pub/pdb/validation_reports/i6/5i6d | HTTPS FTP |
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-Related structure data
Related structure data | 5i7aC 5i7hC 5i7oC 5i7rC 5iw8C 5iwcC 3dkiS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34724.117 Da / Num. of mol.: 4 / Mutation: T2A, K51:PLP-bound Lysine Source method: isolated from a genetically manipulated source Details: CysM, OPS dependent cysteine synthase, covalently bound PLP cofactor at Lys51 Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WP53, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase #2: Chemical | ChemComp-PLP / #3: Chemical | ChemComp-AU6 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.3 % / Description: needle / rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M MgCl2, 0.1M MES pH 6, PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91843 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 21, 2014 |
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: 1.64→47.7 Å / Num. obs: 163557 / % possible obs: 96.9 % / Observed criterion σ(I): 1.8 / Redundancy: 2.4 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.64→1.67 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.8 / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DKI Resolution: 1.64→47.47 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.904 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.079 / 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: 26.632 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→47.47 Å
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Refine LS restraints |
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