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- PDB-3o6t: Mycobacterium tuberculosis thioredoxin C C40S mutant in Complex w... -

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Basic information

Entry
Database: PDB / ID: 3o6t
TitleMycobacterium tuberculosis thioredoxin C C40S mutant in Complex with Quinol Inhibitor PMX464
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT/INHIBITOR / Thioredoxin Fold / Electron Transport / ELECTRON TRANSPORT-INHIBITOR complex
Function / homology
Function and homology information


Cysteine synthesis from O-acetylserine / Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / peptidoglycan-based cell wall / cell redox homeostasis / electron transfer activity / extracellular region ...Cysteine synthesis from O-acetylserine / Cell redox homeostasis / Tolerance by Mtb to nitric oxide produced by macrophages / glutathione disulfide oxidoreductase activity / disulfide oxidoreductase activity / protein-disulfide reductase activity / peptidoglycan-based cell wall / cell redox homeostasis / electron transfer activity / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Chem-PX5 / Thioredoxin / Thioredoxin
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHall, G. / Emsley, J.
CitationJournal: Protein Sci. / Year: 2011
Title: Structure of Mycobacterium tuberculosis thioredoxin in complex with quinol inhibitor PMX464
Authors: Hall, G. / Bradshaw, T.D. / Laughton, C.A. / Stevens, M.F. / Emsley, J.
History
DepositionJul 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin
C: Thioredoxin
D: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5298
Polymers50,7424
Non-polymers7874
Water2,684149
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0793
Polymers12,6851
Non-polymers3932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,6851
Polymers12,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0793
Polymers12,6851
Non-polymers3932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,6851
Polymers12,6851
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.221, 75.095, 65.244
Angle α, β, γ (deg.)90.00, 107.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Thioredoxin / / thioredoxin C / Trx / MPT46


Mass: 12685.497 Da / Num. of mol.: 4 / Mutation: C40S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: TrxC / Plasmid: pGAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: P0A616, UniProt: P9WG67*PLUS
#2: Chemical ChemComp-PX5 / 4-(1,3-benzothiazol-2-yl)-4-hydroxycyclohexa-2,5-dien-1-one / 4-(benzothiazol-2-yl)-4-hydroxycyclohexa-2,5-dienone


Mass: 243.281 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H9NO2S
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND PX5 COVALENTLY BINDS TO CYS37 OF THIOREDOXIN THROUGH A MICHAEL ADDITION ONTO THE BETA- ...THE LIGAND PX5 COVALENTLY BINDS TO CYS37 OF THIOREDOXIN THROUGH A MICHAEL ADDITION ONTO THE BETA-CARBON POSITION OF THE QUINOL RING. THIS BINDING LEADS TO THE LOSS OF PLANARITY IN THE QUINOL RING AND PRODUCES A STRUCTURE WITH A 1,3-CYCLOHEXADIENENE MOIETY, ALTHOUGH THIS COULD BE IN EQUILIBRIUM WITH A CYCLOHEXENONE MOIETY. THIS COMPLEX IS REFERRED AS PMX464 IN THEIR ARTICLE.

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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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Na MES, pH 6.5, 4% PEG 400, 1.6M Ammonium Sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→52.72 Å / Num. all: 22477 / Num. obs: 22477 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.8 / Num. unique all: 3304 / % possible all: 98.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASESphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NOF

3nof


Resolution: 2.4→40.286 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1001 5.14 %RANDOM
Rwork0.1988 ---
all0.236 19458 --
obs0.2019 19462 97.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.771 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3738 Å20 Å23.2596 Å2
2---4.6649 Å20 Å2
3---8.0388 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3288 0 54 149 3491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083394
X-RAY DIFFRACTIONf_angle_d1.1924633
X-RAY DIFFRACTIONf_dihedral_angle_d17.7991265
X-RAY DIFFRACTIONf_chiral_restr0.075580
X-RAY DIFFRACTIONf_plane_restr0.005577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.52650.3051450.23622670X-RAY DIFFRACTION99
2.5265-2.68480.33191370.23522660X-RAY DIFFRACTION98
2.6848-2.8920.32781490.2282653X-RAY DIFFRACTION98
2.892-3.18290.32151310.22022632X-RAY DIFFRACTION98
3.1829-3.64330.25741400.19552638X-RAY DIFFRACTION98
3.6433-4.58910.19561520.16172607X-RAY DIFFRACTION96
4.5891-40.29150.22791470.18732601X-RAY DIFFRACTION94

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