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Yorodumi- PDB-8hfo: Crystal Structure of Mycobacterium smegmatis MshC in Complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hfo | |||||||||
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Title | Crystal Structure of Mycobacterium smegmatis MshC in Complex with Compound 7d | |||||||||
Components | L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase | |||||||||
Keywords | LIGASE / Rossmann fold / Inhibitor | |||||||||
Function / homology | Function and homology information L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase / cysteine-glucosaminylinositol ligase activity / mycothiol biosynthetic process / zinc ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis MC2 155 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å | |||||||||
Authors | Pang, L. / Weeks, S.D. / Strelkov, S.V. | |||||||||
Funding support | Belgium, 2items
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Citation | Journal: Int J Mol Sci / Year: 2022 Title: Structural Basis of Cysteine Ligase MshC Inhibition by Cysteinyl-Sulfonamides. Authors: Pang, L. / Lenders, S. / Osipov, E.M. / Weeks, S.D. / Rozenski, J. / Piller, T. / Cappoen, D. / Strelkov, S.V. / Van Aerschot, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hfo.cif.gz | 179.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hfo.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 8hfo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/8hfo ftp://data.pdbj.org/pub/pdb/validation_reports/hf/8hfo | HTTPS FTP |
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-Related structure data
Related structure data | 8hfmC 8hfnC 3c8zS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 45508.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: mshC, cysS2, MSMEG_4189, MSMEI_4091 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS References: UniProt: A0QZY0, L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase |
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#2: Chemical | ChemComp-XG8 / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Holo protein at 10 mg/mL in 10 mM Tris-HCl pH 7, 100 mM NaCl and 2.5 mM 2-mercaptoethanol was mixed with 1 mM compound 7d and 1 mM TCEP (final concentrations) and incubated on ice for 1 hr. ...Details: Holo protein at 10 mg/mL in 10 mM Tris-HCl pH 7, 100 mM NaCl and 2.5 mM 2-mercaptoethanol was mixed with 1 mM compound 7d and 1 mM TCEP (final concentrations) and incubated on ice for 1 hr. Crystals of MshC in complex with compound 7d were grown in the Morpheus screen by dispensing droplets comprised of 300 nL protein mixture and 150 nL reservoir solution containing PEG550MME 20% (v/v), PEG20000 10% (w/v), Morpheus divalent 60 mM and Morpheus buffer system 3 pH 8.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 2.77→145.59 Å / Num. obs: 21805 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.023 / Rrim(I) all: 0.101 / Χ2: 1.04 / Net I/σ(I): 17.5 / Num. measured all: 438327 |
Reflection shell | Resolution: 2.77→2.92 Å / % possible obs: 100 % / Redundancy: 20.6 % / Rmerge(I) obs: 1.387 / Num. measured all: 65200 / Num. unique obs: 3164 / CC1/2: 0.898 / Rpim(I) all: 0.312 / Rrim(I) all: 1.421 / Χ2: 1.01 / Net I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C8Z Resolution: 2.77→55.03 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 32.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.77→55.03 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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