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- PDB-8c4y: SFX structure of FutA bound to Fe(III) -

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Basic information

Entry
Database: PDB / ID: 8c4y
TitleSFX structure of FutA bound to Fe(III)
ComponentsPutative iron ABC transporter, substrate binding protein
KeywordsMETAL BINDING PROTEIN / Periplasmic iron-binding protein / metal ion binding / iron homeostasis
Function / homologyBacterial extracellular solute-binding protein / Ferric binding protein / iron ion transport / outer membrane-bounded periplasmic space / metal ion binding / : / Putative iron ABC transporter, substrate binding protein
Function and homology information
Biological speciesProchlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBolton, R. / Tews, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
University of Southampton United Kingdom
Diamond Light Source United Kingdom
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron-binding protein FutA from Prochlorococcus.
Authors: Bolton, R. / Machelett, M.M. / Stubbs, J. / Axford, D. / Caramello, N. / Catapano, L. / Maly, M. / Rodrigues, M.J. / Cordery, C. / Tizzard, G.J. / MacMillan, F. / Engilberge, S. / von ...Authors: Bolton, R. / Machelett, M.M. / Stubbs, J. / Axford, D. / Caramello, N. / Catapano, L. / Maly, M. / Rodrigues, M.J. / Cordery, C. / Tizzard, G.J. / MacMillan, F. / Engilberge, S. / von Stetten, D. / Tosha, T. / Sugimoto, H. / Worrall, J.A.R. / Webb, J.S. / Zubkov, M. / Coles, S. / Mathieu, E. / Steiner, R.A. / Murshudov, G. / Schrader, T.E. / Orville, A.M. / Royant, A. / Evans, G. / Hough, M.A. / Owen, R.L. / Tews, I.
#1: Journal: Biorxiv / Year: 2023
Title: A redox switch allows binding of Fe(II) and Fe(III) ions in the cyanobacterial iron binding protein FutA from Prochlorococcus;
Authors: Bolton, R. / Machelett, M. / Stubbs, J. / Axford, D. / Caramello, N. / Catapano, L. / Maly, M. / Rodrigues, M. / Cordery, C. / Tizzard, G. / MacMillan, F. / Engilberge, S. / Stetten, D. / ...Authors: Bolton, R. / Machelett, M. / Stubbs, J. / Axford, D. / Caramello, N. / Catapano, L. / Maly, M. / Rodrigues, M. / Cordery, C. / Tizzard, G. / MacMillan, F. / Engilberge, S. / Stetten, D. / Tosha, T. / Sugimoto, H. / Worrall, J. / Webb, J. / Zubkov, M. / Coles, S. / Mathieu, E. / Steiner, R. / Murshudov, G. / Schrader, T. / Orville, A. / Royant, A. / Evans, G. / Hough, M. / Owen, R. / Tews, I.
History
DepositionJan 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Oct 9, 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

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Assembly

Deposited unit
AAA: Putative iron ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2752
Polymers35,2191
Non-polymers561
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area13570 Å2
Unit cell
Length a, b, c (Å)39.079, 78.290, 47.389
Angle α, β, γ (deg.)90.000, 97.358, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative iron ABC transporter, substrate binding protein


Mass: 35219.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria)
Gene: futA,sfuA, idiA, PMM1164 / Plasmid: pET- 24b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7V0T9
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 294 K / Method: batch mode
Details: Purified protein, diluted crystal seeds, and crystallisation buffer were mixed at a 1:1.5:1.5 ratio. Crystallisation buffer was 25% PEG 3350, 200 mM sodium thiocyanate. Crystal seed stock ...Details: Purified protein, diluted crystal seeds, and crystallisation buffer were mixed at a 1:1.5:1.5 ratio. Crystallisation buffer was 25% PEG 3350, 200 mM sodium thiocyanate. Crystal seed stock was diluted 1:20 in 25% PEG 3350.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.127 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.6→30.1 Å / Num. obs: 37266 / % possible obs: 99.8 % / Redundancy: 618.7 % / Biso Wilson estimate: 12.09 Å2 / CC1/2: 0.99 / R split: 0.053 / Net I/σ(I): 12.1
Reflection shellResolution: 1.6→1.628 Å / Redundancy: 274.5 % / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1877 / CC1/2: 0.91 / R split: 0.089 / % possible all: 100
Serial crystallography measurementPulse duration: 10 fsec. / XFEL pulse repetition rate: 30 Hz
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: Silicon nitride chip / Details: 25600 apertures / Sample dehydration prevention: Sealed with a Mylar film

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→30.096 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.831 / SU ML: 0.063 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.091
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.208 1919 5.149 %
Rwork0.1903 35347 -
all0.191 --
obs-37266 99.791 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.084 Å2
Baniso -1Baniso -2Baniso -3
1--0.025 Å20 Å2-0.503 Å2
2--0.143 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2457 0 1 86 2544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132531
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152479
X-RAY DIFFRACTIONr_angle_refined_deg1.761.6413418
X-RAY DIFFRACTIONr_angle_other_deg1.4611.5885710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94123.101129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49715472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3161515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_nbd_refined0.2050.2504
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.22290
X-RAY DIFFRACTIONr_nbtor_refined0.170.21284
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21315
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.263
X-RAY DIFFRACTIONr_metal_ion_refined0.1160.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.210
X-RAY DIFFRACTIONr_nbd_other0.2330.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2350.212
X-RAY DIFFRACTIONr_mcbond_it1.7581.5221266
X-RAY DIFFRACTIONr_mcbond_other1.7531.5231264
X-RAY DIFFRACTIONr_mcangle_it2.6052.2811586
X-RAY DIFFRACTIONr_mcangle_other2.6042.2811587
X-RAY DIFFRACTIONr_scbond_it2.8611.9421265
X-RAY DIFFRACTIONr_scbond_other2.861.9411266
X-RAY DIFFRACTIONr_scangle_it4.4972.7361832
X-RAY DIFFRACTIONr_scangle_other4.4962.7361833
X-RAY DIFFRACTIONr_lrange_it5.38618.1822798
X-RAY DIFFRACTIONr_lrange_other5.38218.172789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6410.2941460.2812620X-RAY DIFFRACTION99.9639
1.641-1.6860.2781420.2612538X-RAY DIFFRACTION100
1.686-1.7350.3171310.2492452X-RAY DIFFRACTION100
1.735-1.7890.2361330.2352425X-RAY DIFFRACTION100
1.789-1.8470.2271290.212303X-RAY DIFFRACTION100
1.847-1.9120.2491110.1942282X-RAY DIFFRACTION100
1.912-1.9840.2351130.1822191X-RAY DIFFRACTION100
1.984-2.0650.1941170.1672079X-RAY DIFFRACTION100
2.065-2.1570.173980.1732017X-RAY DIFFRACTION100
2.157-2.2620.2031030.181909X-RAY DIFFRACTION100
2.262-2.3840.21990.1831825X-RAY DIFFRACTION100
2.384-2.5290.207860.1851747X-RAY DIFFRACTION100
2.529-2.7030.207860.1961632X-RAY DIFFRACTION100
2.703-2.920.186860.1851513X-RAY DIFFRACTION100
2.92-3.1980.181870.1831389X-RAY DIFFRACTION100
3.198-3.5750.183650.1691281X-RAY DIFFRACTION100
3.575-4.1260.161660.1441102X-RAY DIFFRACTION100
4.126-5.050.213470.172956X-RAY DIFFRACTION100
5.05-7.1270.198520.183728X-RAY DIFFRACTION100
7.127-30.0960.206220.27358X-RAY DIFFRACTION85.0112

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