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- PDB-8hfn: Crystal Structure of Mycobacterium smegmatis MshC in Complex with... -

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Basic information

Entry
Database: PDB / ID: 8hfn
TitleCrystal Structure of Mycobacterium smegmatis MshC in Complex with Compound 7b
ComponentsL-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase
KeywordsLIGASE / 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 / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Mycothiol ligase MshC / Cysteinyl-tRNA synthetase/mycothiol ligase / tRNA synthetases class I, catalytic domain / tRNA synthetases class I (C) catalytic domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
Chem-XGC / L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPang, L. / Weeks, S.D. / Strelkov, S.V.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0A4616N Belgium
Research Foundation - Flanders (FWO)G066619N Belgium
CitationJournal: 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
DepositionNov 11, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0225
Polymers45,5091
Non-polymers5134
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)166.021, 166.021, 51.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein L-cysteine:1D-myo-inositol 2-amino-2-deoxy-alpha-D-glucopyranoside ligase / L-Cys:GlcN-Ins ligase / Mycothiol ligase / MSH ligase


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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-XGC / N-[(3M)-3-(6-methoxypyridin-3-yl)benzene-1-sulfonyl]-L-cysteinamide


Mass: 367.443 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.6 %
Crystal growTemperature: 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 withf 1 mM compound 7b 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 withf 1 mM compound 7b and 1 mM TCEP (final concentrations) and incubated on ice for 1 hr. Crystals of MshC in complex with compound 7b 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.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.98→143.78 Å / Num. obs: 56869 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Χ2: 1.01 / Net I/σ(I): 13.3 / Num. measured all: 579501
Reflection shellResolution: 1.98→2.03 Å / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 1.33 / Num. measured all: 41640 / Num. unique obs: 3944 / CC1/2: 0.867 / Rpim(I) all: 0.427 / Rrim(I) all: 1.397 / Χ2: 1.03 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.19.2refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8Z

3c8z


Resolution: 1.98→54.34 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 2850 5.02 %
Rwork0.185 --
obs0.1861 56794 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→54.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 27 246 3465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043310
X-RAY DIFFRACTIONf_angle_d0.7564520
X-RAY DIFFRACTIONf_dihedral_angle_d5.677482
X-RAY DIFFRACTIONf_chiral_restr0.046485
X-RAY DIFFRACTIONf_plane_restr0.007613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.010.36051460.35292631X-RAY DIFFRACTION100
2.01-2.050.39531500.32632693X-RAY DIFFRACTION100
2.05-2.090.29091350.2982648X-RAY DIFFRACTION100
2.09-2.130.27521370.28012717X-RAY DIFFRACTION100
2.13-2.180.281240.27172662X-RAY DIFFRACTION100
2.18-2.230.28721350.25512700X-RAY DIFFRACTION100
2.23-2.280.26851350.24042669X-RAY DIFFRACTION100
2.28-2.350.26071710.21752663X-RAY DIFFRACTION100
2.35-2.410.251530.2072693X-RAY DIFFRACTION100
2.41-2.490.21621400.20142661X-RAY DIFFRACTION100
2.49-2.580.22451450.20062691X-RAY DIFFRACTION100
2.58-2.680.23391350.19632697X-RAY DIFFRACTION100
2.68-2.810.18581730.20372655X-RAY DIFFRACTION100
2.81-2.960.27231320.20662698X-RAY DIFFRACTION100
2.96-3.140.23131440.21052711X-RAY DIFFRACTION100
3.14-3.380.24581190.20022744X-RAY DIFFRACTION100
3.38-3.720.19611520.17562702X-RAY DIFFRACTION100
3.72-4.260.16611330.13612750X-RAY DIFFRACTION100
4.26-5.370.16761300.14062746X-RAY DIFFRACTION100
5.37-54.340.16221610.15782813X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2978-0.2285-0.01892.0897-0.0891.24370.0661-0.12590.01990.0987-0.06560.39260.0332-0.06740.01670.4883-0.010.00820.4315-0.05840.424663.17212.76196.2007
22.8703-0.33150.68872.0467-0.40820.87540.26510.0732-0.6194-0.1085-0.09850.27520.24970.081-0.1640.49620.0261-0.05020.3605-0.05790.410372.164-12.23375.0549
31.9901-0.21450.09061.62440.17840.98830.0879-0.00850.2823-0.0732-0.10530.3957-0.0994-0.13780.01670.36370.0292-0.00970.3391-0.07090.441556.028715.451-1.5923
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 268 )
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 412 )

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