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- PDB-7pwe: Crystal structure of the glutaredoxin/ferredoxin disulfide reduct... -

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Basic information

Entry
Database: PDB / ID: 7pwe
TitleCrystal structure of the glutaredoxin/ferredoxin disulfide reductase fusion protein from Desulfotalea psychrophila Lsv54
ComponentsFerredoxin-thioredoxin reductase subunit B
KeywordsUNKNOWN FUNCTION / glutaredoxin ferredoxin disulfide reductase ferredocxin thioredoxin reductase enzyme
Function / homology
Function and homology information


ferredoxin-thioredoxin reductase activity / ferredoxin:thioredoxin reductase / oxidoreductase activity, acting on iron-sulfur proteins as donors / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Ferredoxin Thioredoxin Reductase / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin ...Ferredoxin Thioredoxin Reductase / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit / Ferredoxin thioredoxin reductase catalytic beta subunit superfamily / Ferredoxin thioredoxin reductase catalytic beta chain / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / IRON/SULFUR CLUSTER / ferredoxin:thioredoxin reductase
Similarity search - Component
Biological speciesDesulfotalea psychrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.077 Å
AuthorsDidierjean, C. / Mathiot, S. / Rouhier, N.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Inorganics / Year: 2022
Title: Crystal structure of the glutaredoxin/ferredoxin disulfide reductase fusion protein from Desulfotalea psychrophila Lsv54
Authors: Zannini, F. / Mathiot, S. / Couturier, J. / Didierjean, C. / Rouhier, N.
History
DepositionOct 6, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Ferredoxin-thioredoxin reductase subunit B
B: Ferredoxin-thioredoxin reductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,79610
Polymers45,6782
Non-polymers1,1188
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-29 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.6, 49.3, 86
Angle α, β, γ (deg.)90, 116.5, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-356-

HOH

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Components

#1: Protein Ferredoxin-thioredoxin reductase subunit B


Mass: 22838.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfotalea psychrophila (strain LSv54 / DSM 12343) (bacteria)
Strain: LSv54 / DSM 12343 / Gene: DP2155 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6AL91, ferredoxin:thioredoxin reductase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 8
Details: 30% MPD, 10% PEG4000, and 0.1M Imidazole-HCl (JBScreen Classic condition JBS6 B2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.08→41.42 Å / Num. obs: 54939 / % possible obs: 98.7 % / Redundancy: 3 % / Rrim(I) all: 0.037 / Net I/σ(I): 22.81
Reflection shellResolution: 2.08→2.13 Å / Mean I/σ(I) obs: 5.84 / Num. unique obs: 4067 / Rrim(I) all: 0.236

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.077→41.42 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.898 / SU R Cruickshank DPI: 0.203 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.218 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1353 -RANDOM
Rwork0.1911 ---
obs0.1926 28102 99.4 %-
Displacement parametersBiso mean: 37.85 Å2
Baniso -1Baniso -2Baniso -3
1-4.4138 Å20 Å213.0982 Å2
2--1.6577 Å20 Å2
3----6.0715 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.077→41.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 46 327 3506
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083353HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.914538HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1228SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it3353HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion418SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies11HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact3181SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion16.01
LS refinement shellResolution: 2.08→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3605 33 -
Rwork0.2195 --
obs0.2279 563 94.53 %

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