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Yorodumi- PDB-5iwc: Mycobacterium tuberculosis CysM in complex with the Urea-scaffold... -
+Open data
-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] | ||||||
Components | O-phosphoserine sulfhydrylase | ||||||
Keywords | LYASE / Mycobacterium tuberculosis / Cysteine biosynthesis / sulphur metabolism / 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 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Schnell, R. / Maric, S. / Lindqvist, Y. / Schneider, G. | ||||||
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 | 5iwc.cif.gz | 127.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iwc.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 5iwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iwc_validation.pdf.gz | 905.2 KB | Display | wwPDB validaton report |
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Full document | 5iwc_full_validation.pdf.gz | 913.3 KB | Display | |
Data in XML | 5iwc_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5iwc_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iw/5iwc ftp://data.pdbj.org/pub/pdb/validation_reports/iw/5iwc | HTTPS FTP |
-Related structure data
Related structure data | 5i6dC 5i7aC 5i7hC 5i7oC 5i7rC 5iw8C 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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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.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: cysM, Rv1336, MTCY130.21 / Plasmid: pET28a Details (production host): N-terminal His6-tah, 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: 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: 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: 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: 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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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