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- PDB-7p0x: Crystal structure of Thioredoxin reductase from Brugia Malayi -

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Basic information

Entry
Database: PDB / ID: 7p0x
TitleCrystal structure of Thioredoxin reductase from Brugia Malayi
Components(Glutaredoxin domain-containing ...) x 2
KeywordsOXIDOREDUCTASE / Glutaredoxin / flavoprotein / selenocysteine
Function / homology
Function and homology information


ecdysis, collagen and cuticulin-based cuticle / thioredoxin-disulfide reductase (NADPH) / glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin domain profile. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Thioredoxin/glutathione reductase selenoprotein / : / Glutaredoxin domain profile. / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / thioredoxin-disulfide reductase
Similarity search - Component
Biological speciesBrugia malayi (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFata, F. / Ardini, M. / Silvestri, I. / Gabriele, F. / Cheng, Q. / Arner, E.S.J. / Williams, D.L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della Ricerca Italy
CitationJournal: Redox Biol / Year: 2022
Title: Biochemical and structural characterizations of thioredoxin reductase selenoproteins of the parasitic filarial nematodes Brugia malayi and Onchocerca volvulus.
Authors: Fata, F. / Gencheva, R. / Cheng, Q. / Lullo, R. / Ardini, M. / Silvestri, I. / Gabriele, F. / Ippoliti, R. / Bulman, C.A. / Sakanari, J.A. / Williams, D.L. / Arner, E.S.J. / Angelucci, F.
History
DepositionJun 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaredoxin domain-containing protein
B: Glutaredoxin domain-containing protein
C: Glutaredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,15614
Polymers198,2923
Non-polymers2,86411
Water1,11762
1
A: Glutaredoxin domain-containing protein
B: Glutaredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,28412
Polymers132,2062
Non-polymers2,07810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-164 kcal/mol
Surface area45800 Å2
MethodPISA
2
C: Glutaredoxin domain-containing protein
hetero molecules

C: Glutaredoxin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,7454
Polymers132,1742
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10380 Å2
ΔGint-75 kcal/mol
Surface area44890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.921, 258.985, 129.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Glutaredoxin domain-containing ... , 2 types, 3 molecules ABC

#1: Protein Glutaredoxin domain-containing protein / BMA-TRXR-1 / isoform d


Mass: 66102.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CYS 345 in Chains A and B is modified in CSO (S-HYDROXYCYSTEINE)
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: bma-trxr-1, Bma-trxr-1, Bm2025, BM_Bm2025
Production host: synthetic Escherichia coli C321.deltaA (bacteria)
Variant (production host): RF1-depleted / References: UniProt: A0A0J9XPH7
#2: Protein Glutaredoxin domain-containing protein / BMA-TRXR-1 / isoform d


Mass: 66086.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brugia malayi (agent of lymphatic filariasis)
Gene: bma-trxr-1, Bma-trxr-1, Bm2025, BM_Bm2025
Production host: synthetic Escherichia coli C321.deltaA (bacteria)
Variant (production host): RF1-depleted / References: UniProt: A0A0J9XPH7

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Non-polymers , 5 types, 73 molecules

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


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 22% MPD, 0.1M Tris/HCl pH8, 5mM DTT / PH range: 7.5-8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→48.9 Å / Num. obs: 80241 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Net I/σ(I): 28.8
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4505 / CC1/2: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QFA_A, 4TR1

4tr1


Resolution: 2.55→48.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.678 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.397 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 3847 4.8 %RANDOM
Rwork0.1969 ---
obs0.1987 76369 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 285.63 Å2 / Biso mean: 94.366 Å2 / Biso min: 43.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å2-0 Å2-0 Å2
2---0.88 Å2-0 Å2
3---3.09 Å2
Refinement stepCycle: final / Resolution: 2.55→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13255 0 188 62 13505
Biso mean--83.13 61.86 -
Num. residues----1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313733
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712960
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.64318589
X-RAY DIFFRACTIONr_angle_other_deg1.2871.57830109
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80251703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56123.04625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.239152409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5361563
X-RAY DIFFRACTIONr_chiral_restr0.0720.21784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022739
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 306 -
Rwork0.319 5556 -
all-5862 -
obs--100 %
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)
12.0473-0.88970.25972.0567-0.30871.71090.16740.17990.4316-0.0207-0.0493-0.0003-0.3561-0.0355-0.1180.124-0.00440.06940.05970.04940.1397-39.5557-41.5213-16.9941
22.3982-1.49980.35082.707-0.26441.60260.20160.0049-0.2904-0.0256-0.07240.09950.51890.3592-0.12920.27640.0451-0.08590.12760.0010.0524-20.831-78.2147-7.5443
34.6495-0.0088-1.72761.4287-0.20973.6602-0.3214-0.98530.06560.14910.157-0.56230.40521.48210.16440.31440.2375-0.01210.6766-0.06280.4869-53.2772-121.1967-28.5117
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 587
2X-RAY DIFFRACTION2B12 - 586
3X-RAY DIFFRACTION3C14 - 586

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