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- PDB-8cck: Crystal structure of Mycobacterium smegmatis thioredoxin reductas... -

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Basic information

Entry
Database: PDB / ID: 8cck
TitleCrystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with fragment F2X-Entry H07
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / TrxR
Function / homology
Function and homology information


thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / Thioredoxin reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsFuesser, F.T. / Koch, O. / Kuemmel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other governmentTTU 02.906 Germany
CitationJournal: To Be Published
Title: Fragment-based design of mycobacterial thioredoxin reductase inhibitors based on computational exploration of a huge virtual space
Authors: Fuesser, F.T. / Otten, P. / Junker, A. / Kuemmel, D. / Koch, O.
History
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6985
Polymers34,5791
Non-polymers1,1194
Water3,351186
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,39610
Polymers69,1572
Non-polymers2,2388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area8660 Å2
ΔGint-48 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.020, 68.020, 155.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-677-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Thioredoxin reductase


Mass: 34578.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: trxB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FW12

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Non-polymers , 5 types, 190 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-U8X / ~{N}-(4-hydroxyphenyl)-2-pyrazol-1-yl-ethanamide


Mass: 217.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Sodium malonate dibasic monohydrate 2.16 M, Glycerol 10%, pH7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 26, 2021
RadiationMonochromator: Si111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.63→46.92 Å / Num. obs: 52873 / % possible obs: 99.72 % / Redundancy: 9.9 % / Biso Wilson estimate: 26.03 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.6
Reflection shellResolution: 1.63→1.688 Å / Mean I/σ(I) obs: 0.53 / Num. unique obs: 5189 / CC1/2: 0.45

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSXDSAPP 3.1.5data reduction
XSCALEXDSAPP 3.1.5data scaling
PHASER1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8CCI

8cci


Resolution: 1.63→46.92 Å / SU ML: 0.2739 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2419 2638 4.99 %
Rwork0.2143 50223 -
obs0.2157 52861 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.74 Å2
Refinement stepCycle: LAST / Resolution: 1.63→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 76 186 2568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832465
X-RAY DIFFRACTIONf_angle_d1.06493354
X-RAY DIFFRACTIONf_chiral_restr0.0642377
X-RAY DIFFRACTIONf_plane_restr0.0101436
X-RAY DIFFRACTIONf_dihedral_angle_d13.2296352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.660.43811360.44982494X-RAY DIFFRACTION94.88
1.66-1.690.45061230.42492576X-RAY DIFFRACTION99.93
1.69-1.720.41341590.42252595X-RAY DIFFRACTION99.93
1.72-1.760.43191440.41272623X-RAY DIFFRACTION99.82
1.76-1.80.38871490.37582619X-RAY DIFFRACTION99.96
1.8-1.850.36791220.35352629X-RAY DIFFRACTION99.93
1.85-1.90.37561310.33632607X-RAY DIFFRACTION99.96
1.9-1.950.32991440.30242597X-RAY DIFFRACTION99.93
1.95-2.020.26621310.28522653X-RAY DIFFRACTION99.96
2.02-2.090.31991460.25182608X-RAY DIFFRACTION99.93
2.09-2.170.2411530.2192612X-RAY DIFFRACTION100
2.17-2.270.21961840.21322625X-RAY DIFFRACTION100
2.27-2.390.21491110.19632650X-RAY DIFFRACTION99.93
2.39-2.540.22351200.20312671X-RAY DIFFRACTION100
2.54-2.740.2051380.18372684X-RAY DIFFRACTION100
2.74-3.010.19831260.19222674X-RAY DIFFRACTION100
3.01-3.450.20671340.18242710X-RAY DIFFRACTION100
3.45-4.340.19791350.15522731X-RAY DIFFRACTION100
4.34-46.920.22461520.192865X-RAY DIFFRACTION99.9
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)
12.05934846728-1.267078051-1.140578082862.510184228771.658175569133.86984503991-0.030990721567-0.0952748462539-0.06144873707760.09445068122480.144346743206-0.0859293161246-0.04225162004560.336299065683-0.1254051327020.115052780774-0.0382162338168-0.005517317126870.201219092296-0.02094963437150.16525443089622.437673379.1108875015-13.5503295283
21.2568905913-2.553354708680.3106781071425.965287204080.006965249121840.5271378586150.09081502114610.05059204360810.004128782437180.254211614813-0.00822638327798-0.2671581565970.180482250678-0.0364981670372-0.02411773355510.339152211588-0.0624102981862-0.06903222054010.3127757405360.02577306884440.25596146934420.842289366-9.18702069588-9.55915906371
32.508893519120.1600929621950.5739994185884.20048933856-2.171503236888.59996949056-0.159464107029-0.143471477912-0.227173437127-0.2447844842550.3016518065490.2089580897760.0249664075812-0.55170857929-0.1107596387070.3535094825010.0412315175461-0.008383573355650.3417126197710.07678198134830.29486930896415.4457014307-25.642914437-8.09575343831
41.65811308493-1.564379467-0.3049059977582.6468286620.5373661633721.19363376294-0.0254383882509-0.0713269442564-0.165984232930.1344499669030.0229807237290.2838909937070.0311671766432-0.179232984999-0.01159856906030.130282821802-0.02271823278980.002340568861520.2224864445-0.009021594218610.1663145099629.600903756771.80421861059-15.6400742698
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 6 through 107 )6 - 1071 - 102
22chain 'A' and (resid 108 through 145 )108 - 145103 - 140
33chain 'A' and (resid 146 through 231 )146 - 231141 - 226
44chain 'A' and (resid 232 through 310 )232 - 310227 - 305

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