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- PDB-8fx9: Crystal strucutre of Mycobacterium tuberculosis Mycothiol-S-trans... -

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Basic information

Entry
Database: PDB / ID: 8fx9
TitleCrystal strucutre of Mycobacterium tuberculosis Mycothiol-S-transferase enzyme
ComponentsMycothiol-S-transferase
KeywordsTRANSFERASE / Mycothiol / DinB superfamily / Apo / Metalloenzyme
Function / homologyProtein of unknown function DUF664 / Mycothiol-S-transferase / DinB/YfiT-like putative metalloenzymes / metal ion binding / Conserved protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLindenberger, J.J. / Jayasinghe, Y.P. / Ronning, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI151924 United States
CitationJournal: Rsc Med Chem / Year: 2023
Title: The Mycobacterium tuberculosis mycothiol S -transferase is divalent metal-dependent for mycothiol binding and transfer.
Authors: Jayasinghe, Y.P. / Banco, M.T. / Lindenberger, J.J. / Favrot, L. / Palcekova, Z. / Jackson, M. / Manabe, S. / Ronning, D.R.
History
DepositionJan 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycothiol-S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8252
Polymers18,7901
Non-polymers351
Water3,837213
1
A: Mycothiol-S-transferase
hetero molecules

A: Mycothiol-S-transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6514
Polymers37,5802
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area2890 Å2
ΔGint-39 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.377, 98.891, 49.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Mycothiol-S-transferase


Mass: 18789.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0443 / Production host: Escherichia coli (E. coli) / References: UniProt: O53728
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 0.2 M Magnesium chloride, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.36→50 Å / Num. obs: 31576 / % possible obs: 99.89 % / Redundancy: 12.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.61
Reflection shellResolution: 1.36→1.41 Å / Rmerge(I) obs: 0.49 / Num. unique obs: 2669 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→29.43 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2157 1993 6.33 %
Rwork0.1872 --
obs0.189 31474 89.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→29.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 1 213 1537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061405
X-RAY DIFFRACTIONf_angle_d0.771928
X-RAY DIFFRACTIONf_dihedral_angle_d3.84199
X-RAY DIFFRACTIONf_chiral_restr0.064216
X-RAY DIFFRACTIONf_plane_restr0.008254
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.29181150.24011701X-RAY DIFFRACTION73
1.39-1.430.2721360.2292019X-RAY DIFFRACTION87
1.43-1.470.23711500.21812229X-RAY DIFFRACTION96
1.47-1.520.24131580.19982326X-RAY DIFFRACTION99
1.52-1.580.22351560.18142299X-RAY DIFFRACTION100
1.58-1.640.17541550.17452317X-RAY DIFFRACTION100
1.64-1.710.20771600.17612343X-RAY DIFFRACTION100
1.71-1.80.21611580.18082337X-RAY DIFFRACTION100
1.8-1.920.2741200.22451780X-RAY DIFFRACTION76
1.92-2.060.24141300.21171901X-RAY DIFFRACTION81
2.06-2.210.20061130.18061677X-RAY DIFFRACTION98
2.29-2.60.20721440.18492155X-RAY DIFFRACTION99
2.6-3.280.22691620.18372392X-RAY DIFFRACTION100
3.28-29.430.18661360.16932005X-RAY DIFFRACTION80

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