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- PDB-9hi3: C-terminal domain of pectobacterial FusB in complex with spinach ... -

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Basic information

Entry
Database: PDB / ID: 9hi3
TitleC-terminal domain of pectobacterial FusB in complex with spinach ferredoxin 1
ComponentsProtein TonB,Ferredoxin-1, chloroplastic
KeywordsPROTEIN TRANSPORT / TonB / TonB-dependent nutrient import / iron uptake / iron acquisition / protein uptake
Function / homology
Function and homology information


energy transducer activity / siderophore transport / plasma membrane protein complex / chloroplast stroma / electron transport chain / transmembrane transport / 2 iron, 2 sulfur cluster binding / protein transport / outer membrane-bounded periplasmic space / electron transfer activity / metal ion binding
Similarity search - Function
Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain ...Gram-negative bacterial TonB protein / : / TonB C-terminal domain profile. / TonB, C-terminal / Gram-negative bacterial TonB protein C-terminal / TonB/TolA, C-terminal / Ferredoxin [2Fe-2S], plant / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / : / NICKEL (II) ION / Ferredoxin-1, chloroplastic / Protein TonB
Similarity search - Component
Biological speciesPectobacterium carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWojnowska, M. / Bogucka, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Cambridge United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: Receptor-substrate competition for the TonB homologue FusB suggests a model for ferredoxin import in Pectobacterium spp
Authors: Wojnowska, M. / Flores, V. / Yelland, T. / Fisher, S.R. / Bogucka, A. / Stott, K. / Walker, D.
History
DepositionNov 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein TonB,Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6624
Polymers21,3891
Non-polymers2743
Water3,765209
1
A: Protein TonB,Ferredoxin-1, chloroplastic
hetero molecules

A: Protein TonB,Ferredoxin-1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3248
Polymers42,7772
Non-polymers5476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3900 Å2
ΔGint-40 kcal/mol
Surface area17120 Å2
Unit cell
Length a, b, c (Å)66.678, 67.446, 85.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

21A-603-

HOH

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Components

#1: Protein Protein TonB,Ferredoxin-1, chloroplastic / Ferredoxin I / Fd I


Mass: 21388.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum (bacteria) / Gene: ECA0877, PETF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D8U5, UniProt: P00221
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M HEPES,0.05M MOPS pH 7.5, 2M divalent cations (0.005M Manganese(II) chloride, 0.005M Cobalt(II) chloride , 0.005M Nickel(II) chloride, 0.005M Zinc acetate), 0.1 M monosaccharides (0.2 M ...Details: 0.05M HEPES,0.05M MOPS pH 7.5, 2M divalent cations (0.005M Manganese(II) chloride, 0.005M Cobalt(II) chloride , 0.005M Nickel(II) chloride, 0.005M Zinc acetate), 0.1 M monosaccharides (0.2 M xylitol, 0.2 M D-fructose, 0.2 M D-sorbitol, 0.2 M myo-inositol, 0.2 M L-rhamnose monohydrate), 20% PEGMME550, 10% PEG 20k

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→47.42 Å / Num. obs: 21660 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 1 / Rrim(I) all: 0.152 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.73 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 999 / CC1/2: 0.8 / Rrim(I) all: 1.156

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.42 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20536 1026 4.7 %RANDOM
Rwork0.15923 ---
obs0.16146 20601 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.182 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å20 Å2
2--2.08 Å2-0 Å2
3----1.46 Å2
Refinement stepCycle: 1 / Resolution: 1.7→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 2 209 1715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0121598
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161456
X-RAY DIFFRACTIONr_angle_refined_deg2.0131.8142178
X-RAY DIFFRACTIONr_angle_other_deg1.1491.7753368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.131511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5810260
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021966
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02358
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0782.103826
X-RAY DIFFRACTIONr_mcbond_other2.0732.104826
X-RAY DIFFRACTIONr_mcangle_it2.7553.7651043
X-RAY DIFFRACTIONr_mcangle_other2.7573.7661044
X-RAY DIFFRACTIONr_scbond_it3.7072.44772
X-RAY DIFFRACTIONr_scbond_other3.7142.445769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5324.3071132
X-RAY DIFFRACTIONr_long_range_B_refined6.93427.721833
X-RAY DIFFRACTIONr_long_range_B_other6.78725.981773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å
RfactorNum. reflection% reflection
Rfree0.314 62 -
Rwork0.267 1444 -
obs--96.11 %

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