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

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Basic information

Entry
Database: PDB / ID: 8ccm
TitleCrystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with Compound 2-06
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 / MALONATE ION / : / Thioredoxin reductase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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. / Kuemmel, D. / Koch, O. / Otten, P. / Junker, A.
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)36,03610
Polymers34,5791
Non-polymers1,4589
Water3,333185
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,07320
Polymers69,1572
Non-polymers2,91518
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10000 Å2
ΔGint-76 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.150, 68.150, 154.890
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-685-

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 , 7 types, 194 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-U9C / ~{N}6-(4-aminophenyl)-1,2-benzothiazole-3,6-diamine


Mass: 256.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N4S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 59.04 %
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: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 14, 2022
RadiationMonochromator: Si111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.73→46.94 Å / Num. obs: 44354 / % possible obs: 99.78 % / Redundancy: 9.9 % / Biso Wilson estimate: 28.47 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.81
Reflection shellResolution: 1.73→1.792 Å / Mean I/σ(I) obs: 0.54 / Num. unique obs: 4394 / CC1/2: 0.49

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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: 1.73→38.86 Å / SU ML: 0.2839 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2236 2097 4.74 %
Rwork0.2008 42188 -
obs0.2019 44285 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.33 Å2
Refinement stepCycle: LAST / Resolution: 1.73→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 95 185 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822514
X-RAY DIFFRACTIONf_angle_d0.98363427
X-RAY DIFFRACTIONf_chiral_restr0.0621383
X-RAY DIFFRACTIONf_plane_restr0.0091467
X-RAY DIFFRACTIONf_dihedral_angle_d12.984381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.44761370.44372759X-RAY DIFFRACTION99.72
1.77-1.810.41551370.40992757X-RAY DIFFRACTION99.48
1.81-1.860.41391370.3532759X-RAY DIFFRACTION99.76
1.86-1.920.31451380.32882775X-RAY DIFFRACTION99.73
1.92-1.980.30591390.30692789X-RAY DIFFRACTION99.69
1.98-2.050.31851380.28162777X-RAY DIFFRACTION99.76
2.05-2.130.27751390.24642785X-RAY DIFFRACTION99.86
2.13-2.230.23441380.2142785X-RAY DIFFRACTION99.83
2.23-2.350.26951400.20252803X-RAY DIFFRACTION99.83
2.35-2.50.23041390.19512799X-RAY DIFFRACTION99.86
2.5-2.690.20111400.19742820X-RAY DIFFRACTION99.93
2.69-2.960.20451420.18442843X-RAY DIFFRACTION99.87
2.96-3.390.19951400.182839X-RAY DIFFRACTION99.97
3.39-4.260.17981430.1492880X-RAY DIFFRACTION99.97
4.27-38.860.18781500.17033018X-RAY DIFFRACTION99.62
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)
14.023488772230.281922222599-2.3476369581.03736464815-0.1437281229563.788513691320.0923816135065-0.1868011314420.1136866157730.07859518116560.0399841589909-0.0394873038388-0.2845369159230.101475195949-0.1494009009150.29695881054-0.008805929529250.01185796940280.192054155377-0.01650092408170.1889171943733.5204790901323.992230364912.2841039112
23.78012189565-1.597659244472.133859471920.711810874965-1.358462094131.073200943240.262389288709-0.0378244808375-0.146696987802-0.17150033672-0.183910976522-0.04105570507560.1529369951370.227805009562-0.09489952588560.5490281515160.0211450388471-0.05394460237420.489439095787-0.01296407237480.29301055149526.03627731384.6322047417717.3157894392
34.78422317881-0.296463165106-1.545924616161.828653774390.080363116393.96226562566-0.0255947521044-0.0775664847071-0.2757425921080.05703580711720.01511767039150.1434479774880.345063395464-0.1944992838930.0002241523791610.265897808798-0.042824250828-0.005936523322940.201443307718-0.007445345370620.188632780078-0.5324080138939.590385001158.94839175256
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 244 )108 - 244103 - 239
33chain 'A' and (resid 245 through 310 )245 - 310240 - 305

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