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Yorodumi- PDB-5i7r: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -
+Open data
-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] | ||||||
Components | O-phosphoserine sulfhydrylase | ||||||
Keywords | LYASE / Mycobacterium tuberculosis / Cysteine biosynthesis / sulphur metabolism / inhibitor | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 | 5i7r.cif.gz | 136.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5i7r.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 5i7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/5i7r ftp://data.pdbj.org/pub/pdb/validation_reports/i7/5i7r | HTTPS FTP |
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-Related structure data
Related structure data | 5i6dC 5i7aC 5i7hC 5i7oC 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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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.) Mycobacterium tuberculosis (bacteria) / Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a Details (production host): N-terminal His6-tag, Thrombin site for tag removal Production host: Escherichia coli BL21(DE3) (bacteria) 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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