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- PDB-8rk1: Crystal structure of FutA bound to Fe(III) solved by neutron diff... -

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Basic information

Entry
Database: PDB / ID: 8rk1
TitleCrystal structure of FutA bound to Fe(III) solved by neutron diffraction
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)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.095 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
DepositionDec 22, 2023Deposition site: PDBE / Processing site: PDBE
SupersessionJan 17, 2024ID: 8OEN
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: 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
Revision 1.2Mar 27, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Oct 16, 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
A: Putative iron ABC transporter, substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2752
Polymers35,2191
Non-polymers561
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.542, 78.316, 47.893
Angle α, β, γ (deg.)90, 97.365, 90
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.: 109 / 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: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 294 K / Method: batch mode
Details: Purified protein and crystallisation buffer were mixed at a 1:1 ratio. Crystallisation buffer was 20% PEG 3350, 200 mM sodium thiocyanate.

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Data collection

DiffractionMean temperature: 294 K / Serial crystal experiment: N
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 3.1 Å
DetectorType: BIODIFF / Detector: IMAGE PLATE / Date: Feb 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 3.1 Å / Relative weight: 1
ReflectionResolution: 2.095→50 Å / Num. obs: 13758 / % possible obs: 80.8 % / Redundancy: 1.9 % / CC1/2: 0.971 / Rpim(I) all: 0.106 / Rrim(I) all: 0.168 / Net I/σ(I): 4.6
Reflection shellResolution: 2.095→2.18 Å / Num. unique obs: 886 / CC1/2: 0.716 / Rpim(I) all: 0.334 / Rrim(I) all: 0.473 / % possible all: 52.4

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Processing

RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.095→24.95 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.869 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.176 / SU B: 10.369 / SU ML: 0.267 / Average fsc free: 0.9545 / Average fsc work: 0.976 / Cross valid method: FREE R-VALUE / ESU R Free: 0.357
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2425 698 5.077 %
Rwork0.1776 13050 -
all0.181 --
obs-13748 80.412 %
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: 22.465 Å2
Baniso -1Baniso -2Baniso -3
1--0.134 Å2-0 Å2-0.184 Å2
2--0.197 Å20 Å2
3----0.014 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
NEUTRON DIFFRACTIONr_bond_refined_d0.0280.0145311
NEUTRON DIFFRACTIONr_angle_refined_deg0.951.6319360
NEUTRON DIFFRACTIONr_dihedral_angle_1_deg6.3575319
NEUTRON DIFFRACTIONr_dihedral_angle_2_deg7.6577.05690
NEUTRON DIFFRACTIONr_dihedral_angle_3_deg14.61910735
NEUTRON DIFFRACTIONr_dihedral_angle_6_deg14.92610136
NEUTRON DIFFRACTIONr_chiral_restr0.0610.2382
NEUTRON DIFFRACTIONr_gen_planes_refined0.0060.023591
NEUTRON DIFFRACTIONr_nbd_refined0.190.22136
NEUTRON DIFFRACTIONr_nbtor_refined0.1630.21384
NEUTRON DIFFRACTIONr_xyhbond_nbd_refined0.2030.2130
NEUTRON DIFFRACTIONr_metal_ion_refined0.0220.22
NEUTRON DIFFRACTIONr_symmetry_nbd_refined0.2260.250
NEUTRON DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2270.212
NEUTRON DIFFRACTIONr_mcbond_it1.0211.9011867
NEUTRON DIFFRACTIONr_mcangle_it1.7693.2352792
NEUTRON DIFFRACTIONr_scbond_it1.2832.3523443
NEUTRON DIFFRACTIONr_scangle_it2.3223.6616567
NEUTRON DIFFRACTIONr_lrange_it6.80322.7585806
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.095-2.1490.33290.2995560.312440.9210.94447.02570.287
2.149-2.2070.4310.2656730.26912210.8910.95657.65770.264
2.207-2.2710.282480.2427350.24411890.9540.96265.85370.243
2.271-2.340.259420.2178670.21911680.9560.96877.82530.207
2.34-2.4160.236500.1868360.18911110.9650.97779.7480.179
2.416-2.50.232480.1838550.18510920.9670.97882.69230.174
2.5-2.5930.284530.2087790.21310120.940.96982.21340.213
2.593-2.6980.319390.2177480.22110090.920.96877.9980.225
2.698-2.8170.254490.2088090.2119760.9530.97187.90980.215
2.817-2.9520.168340.177960.179100.9750.98291.20880.164
2.952-3.1090.291410.177760.1778830.9590.98292.52550.166
3.109-3.2950.213330.1657670.1678440.9670.98494.78670.164
3.295-3.5180.205360.1527090.1557790.970.98795.63540.154
3.518-3.7940.303290.1496680.1567320.9510.98695.21860.156
3.794-4.1460.235370.1446080.1496840.9570.98894.29820.155
4.146-4.620.207270.1245360.1286110.9740.99192.1440.14
4.62-5.3040.199260.1344750.1375510.9760.9990.92560.149
5.304-6.4240.207290.1543810.1574670.9720.98687.79440.181
6.424-8.7980.10490.1233000.1223650.9940.99184.65750.154
8.798-24.950.14380.1841760.1822380.9840.98577.31090.242

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