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- PDB-7qp5: Crystal Structure of E. coli FhuF -

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Basic information

Entry
Database: PDB / ID: 7qp5
TitleCrystal Structure of E. coli FhuF
ComponentsFerric iron reductase protein FhuF
KeywordsOXIDOREDUCTASE / Ferric Siderophore Reductase / Iron-Sulphur protein / Iron uptake
Function / homology
Function and homology information


ferric-chelate reductase activity / reductive iron assimilation / siderophore-dependent iron import into cell / oxidoreductase activity, acting on metal ions / 2 iron, 2 sulfur cluster binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Ferric iron reductase / Ferric iron reductase, C-terminal / FhuF 2Fe-2S C-terminal domain / Ferric iron reductase FhuF domain / Ferric iron reductase FhuF-like transporter
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Ferric siderophore reductase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsTrindade, I.B. / Rollo, F. / Matias, P.M. / Moe, E. / Louro, R.O.
Funding support Portugal, European Union, 3items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPD/BD/135187/2017 Portugal
European Commission810856European Union
Fundacao para a Ciencia e a TecnologiaUIDB/04612/2020 and UIDP/04612/2020 Portugal
CitationJournal: Biorxiv / Year: 2023
Title: The structure of a novel ferredoxin: FhuF, a ferric-siderophore reductase from E. coli K-12 with a novel 2Fe-2S cluster coordination
Authors: Trindade, I.B. / Rollo, F. / Todorovic, S. / Catarino, T. / Moe, E. / Matias, P.M. / Piccioli, M. / Louro, R.O.
History
DepositionJan 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / struct_ncs_dom_lim
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization ..._pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric iron reductase protein FhuF
B: Ferric iron reductase protein FhuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4264
Polymers56,0752
Non-polymers3522
Water2,828157
1
A: Ferric iron reductase protein FhuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2132
Polymers28,0371
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric iron reductase protein FhuF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2132
Polymers28,0371
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.912, 73.574, 71.878
Angle α, β, γ (deg.)90.000, 113.440, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and resid 21 through 301)

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNLEULEUAA21 - 2614 - 244
d_12FESFESFESFESAC301
d_21GLNGLNLEULEUBB21 - 2614 - 244
d_22FESFESFESFESBD301

NCS oper: (Code: givenMatrix: (0.281609956578, -0.00462675931479, 0.959517808826), (0.000584849470999, -0.999987361124, -0.00499355012259), (0.959528785554, 0.0019674069161, -0.281603691387)Vector: - ...NCS oper: (Code: given
Matrix: (0.281609956578, -0.00462675931479, 0.959517808826), (0.000584849470999, -0.999987361124, -0.00499355012259), (0.959528785554, 0.0019674069161, -0.281603691387)
Vector: -6.68050283037, -44.8236187438, -5.15462655557)

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Components

#1: Protein Ferric iron reductase protein FhuF


Mass: 28037.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: fhuF, yjjS, b4367, JW4331 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39405
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Fe2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.78 % / Description: Thick plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: Protein concentration 50 MG/ML, 0.2 M MGCL2.6H2O, 0.1 M TRIS-HCL PH 8.5, 30% W/V PEG 4000, Hanging drop vapor diffusion; 2 microliters protein + 2 microliters reservoir equilibrated against ...Details: Protein concentration 50 MG/ML, 0.2 M MGCL2.6H2O, 0.1 M TRIS-HCL PH 8.5, 30% W/V PEG 4000, Hanging drop vapor diffusion; 2 microliters protein + 2 microliters reservoir equilibrated against 500 microliters reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.92→65.95 Å / Num. obs: 25252 / % possible obs: 52.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.05 / Net I/σ(I): 9.3
Reflection shellResolution: 1.92→2.11 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1127 / CC1/2: 0.56 / Rpim(I) all: 0.492 / % possible all: 10.7

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Processing

Software
NameVersionClassification
PHENIX1.20_4438refinement
XDSFeb 5, 2021data reduction
STARANISO1.0.5data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ALPHA FOLD MODEL

Resolution: 1.92→65.95 Å / SU ML: 0.2721 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.1797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.252 1319 5.23 %
Rwork0.2093 23925 -
obs0.2115 25244 59.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.81 Å2
Refinement stepCycle: LAST / Resolution: 1.92→65.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3879 0 8 157 4044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263984
X-RAY DIFFRACTIONf_angle_d0.55885431
X-RAY DIFFRACTIONf_chiral_restr0.0386617
X-RAY DIFFRACTIONf_plane_restr0.0045693
X-RAY DIFFRACTIONf_dihedral_angle_d12.86111472
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.213809848111 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-20.3789140.3018188X-RAY DIFFRACTION4.32
2-2.090.3156480.2859848X-RAY DIFFRACTION18.89
2.09-2.20.3116730.27111531X-RAY DIFFRACTION34
2.2-2.340.30341090.25642049X-RAY DIFFRACTION45.84
2.34-2.520.31511500.26232625X-RAY DIFFRACTION58.51
2.52-2.770.29121860.26723354X-RAY DIFFRACTION74.48
2.77-3.170.29812400.23354256X-RAY DIFFRACTION94.61
3.17-3.990.24622390.18854518X-RAY DIFFRACTION99.44
3.99-65.950.20312600.17564556X-RAY DIFFRACTION99.3

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