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

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Basic information

Entry
Database: PDB / ID: 8ccl
TitleCrystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with fragment F2X-Entry A09
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / TrxR
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / nucleotide binding / 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 / MALONATE ION / : / Thioredoxin reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 20, 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

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8608
Polymers34,5791
Non-polymers1,2827
Water3,297183
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,72116
Polymers69,1572
Non-polymers2,56314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area9370 Å2
ΔGint-55 kcal/mol
Surface area24520 Å2
Unit cell
Length a, b, c (Å)67.890, 67.890, 155.400
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-508-

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 , 6 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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-U8O / [1,2]thiazolo[5,4-b]pyridin-3-amine


Mass: 151.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
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 PILATUS 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: 1.85→46.88 Å / Num. obs: 36273 / % possible obs: 99.81 % / Redundancy: 9.9 % / Biso Wilson estimate: 27.98 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.42
Reflection shellResolution: 1.85→1.92 Å / Mean I/σ(I) obs: 0.54 / Num. unique obs: 3546 / CC1/2: 0.43

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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: 1.85→46.88 Å / SU ML: 0.2767 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2317 1803 4.98 %
Rwork0.1962 34423 -
obs0.1979 36226 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.77 Å2
Refinement stepCycle: LAST / Resolution: 1.85→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 85 183 2574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822480
X-RAY DIFFRACTIONf_angle_d1.03583375
X-RAY DIFFRACTIONf_chiral_restr0.063378
X-RAY DIFFRACTIONf_plane_restr0.0112440
X-RAY DIFFRACTIONf_dihedral_angle_d13.4622354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.41991360.41052621X-RAY DIFFRACTION99.78
1.9-1.960.41141360.34682590X-RAY DIFFRACTION99.67
1.96-2.020.29381360.30622595X-RAY DIFFRACTION99.82
2.02-2.090.30781370.28212597X-RAY DIFFRACTION99.64
2.09-2.170.28511380.2372624X-RAY DIFFRACTION99.78
2.18-2.270.27781380.22062622X-RAY DIFFRACTION99.93
2.27-2.390.24641350.20212628X-RAY DIFFRACTION99.93
2.39-2.540.20071370.19512613X-RAY DIFFRACTION99.89
2.54-2.740.21551390.18212655X-RAY DIFFRACTION99.89
2.74-3.020.21281390.17382644X-RAY DIFFRACTION99.93
3.02-3.450.231410.16832685X-RAY DIFFRACTION99.96
3.45-4.350.16441420.14822708X-RAY DIFFRACTION100
4.35-46.880.23441490.18282841X-RAY DIFFRACTION99.8
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)
12.30199550965-1.05401053348-1.269727941442.723266971321.460204640484.184164347890.0364259104704-0.1301325676650.01080179974840.05745629852020.0917997449829-0.118404781171-0.04386546151710.354174265232-0.1380495779290.131091532142-0.0425243614943-0.014975078450.215882031855-0.02491200771260.14214226179122.44819487329.10206684354-13.5501508628
22.63804641389-4.593908396451.856106600439.42560608765-3.138192765883.16900474032-0.06043176347450.00967726100749-0.08291784324650.8699801886460.0509191077618-0.1173762850150.147754511755-0.03819336261480.04552818509270.366440224879-0.0307327444627-0.009243606326070.269070621596-0.01175984872220.1844248159616.9378566673-3.32980036256-6.06939042721
32.850733430140.556305574345-0.5999997849344.50381087544-2.086176499586.76530914769-0.2183587592730.128421903571-0.1059217588-0.2540367341030.2791281618540.177852509745-0.0616065640849-0.172581572321-0.04560504312530.444775341630.0189270748731-0.04727114009950.408220545150.06641155258950.2882281385116.8445155994-24.2347280598-8.98939785555
41.76192913432-1.84483932858-0.2884771653512.860549303360.819999691820.932490154324-0.013051582014-0.0443027346658-0.170137219050.0831744402673-0.01420418667660.2710744516530.00349767098663-0.1524690015940.01181935805860.160764888935-0.0285878117545-0.0004174786021930.267155740558-0.008618577477690.1583359969559.611366301581.70413494216-15.6086045403
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 128 )108 - 128103 - 123
33chain 'A' and (resid 129 through 231 )129 - 231124 - 226
44chain 'A' and (resid 232 through 310 )232 - 310227 - 305

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