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- PDB-8oei: SFX structure of FutA after an accumulated dose of 350 kGy -

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Entry
Database: PDB / ID: 8oei
TitleSFX structure of FutA after an accumulated dose of 350 kGy
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: 1.65 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
DepositionMar 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 2.0Mar 13, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / citation / citation_author / entity / pdbx_audit_support / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct / struct_conn / struct_mon_prot_cis
Item: _cell.angle_alpha / _cell.angle_gamma ..._cell.angle_alpha / _cell.angle_gamma / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_number_of_molecules / _pdbx_audit_support.country / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_d_res_low / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.pdbx_total_number_of_bins_used / _refine_ls_shell.percent_reflns_obs / _refine_ls_shell.wR_factor_R_work / _reflns.d_resolution_low / _software.version / _struct.title / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_mon_prot_cis.pdbx_omega_angle
Description: Atoms with unrealistic or zero occupancies / Provider: author / Type: Coordinate replacement
Revision 2.1Mar 27, 2024Group: Database references / Category: citation / citation_author

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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
Water1,928107
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 area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.366, 78.22, 48.025
Angle α, β, γ (deg.)90, 97.903, 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.: 107 / 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: 2.08 Å3/Da / Density % sol: 40.98 %
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: 1.126 Å
DetectorType: MPCCD / Detector: CCD / Date: May 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.126 Å / Relative weight: 1
ReflectionResolution: 1.65→32.441 Å / Num. obs: 34653 / % possible obs: 100 % / Redundancy: 165.2 % / Biso Wilson estimate: 20.98 Å2 / CC1/2: 0.97 / R split: 0.134 / Net I/σ(I): 3.7
Reflection shellResolution: 1.65→1.679 Å / Redundancy: 82.4 % / Mean I/σ(I) obs: 0.43 / Num. unique obs: 1676 / CC1/2: 0.4 / Rpim(I) all: 0.691 / % 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
REFMAC5.8.0425refinement
DIALSdata reduction
cctbx.xfel.mergedata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→32.441 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.173 / SU B: 2.583 / SU ML: 0.083 / Average fsc free: 0.9717 / Average fsc work: 0.978 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1885 1786 5.154 %
Rwork0.1599 32867 -
all0.161 --
obs-34653 99.957 %
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: 27.641 Å2
Baniso -1Baniso -2Baniso -3
1-0.295 Å2-0 Å2-0.303 Å2
2--0.161 Å2-0 Å2
3----0.358 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.441 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2460 0 1 107 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162554
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.8293555
X-RAY DIFFRACTIONr_angle_other_deg0.5381.7865881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.619516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70810487
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.8610121
X-RAY DIFFRACTIONr_chiral_restr0.0780.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023139
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_nbd_refined0.2210.2502
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.22210
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21300
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.274
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2770.26
X-RAY DIFFRACTIONr_nbd_other0.2050.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1440.23
X-RAY DIFFRACTIONr_mcbond_it2.0192.361307
X-RAY DIFFRACTIONr_mcbond_other2.0022.3611306
X-RAY DIFFRACTIONr_mcangle_it2.8424.2431646
X-RAY DIFFRACTIONr_mcangle_other2.8414.2421647
X-RAY DIFFRACTIONr_scbond_it3.8342.9261325
X-RAY DIFFRACTIONr_scbond_other3.8312.9271325
X-RAY DIFFRACTIONr_scangle_it6.135.0981909
X-RAY DIFFRACTIONr_scangle_other6.1295.0981910
X-RAY DIFFRACTIONr_lrange_it7.07323.5382883
X-RAY DIFFRACTIONr_lrange_other7.07123.0772867
LS refinement shell

Refine-ID: X-RAY 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
1.65-1.6930.2871430.27523730.27525190.9440.94399.88090.281
1.693-1.7390.2431210.2423660.2424870.9580.9581000.246
1.739-1.7890.2261200.21923240.2224440.9660.9681000.225
1.789-1.8440.1881280.19121870.19123150.9750.9751000.193
1.844-1.9040.2281060.18421890.18622950.9680.9791000.184
1.904-1.9710.2181140.17420760.17621900.9720.981000.172
1.971-2.0450.1861130.15420060.15621190.9770.9851000.155
2.045-2.1280.1671000.14619490.14720490.9830.9871000.147
2.128-2.2220.199920.15618860.15819780.9720.9851000.16
2.222-2.330.17940.15217770.15318710.9810.9861000.157
2.33-2.4560.201930.14816940.1517870.9720.9871000.156
2.456-2.6040.219790.15116160.15416950.9760.9871000.162
2.604-2.7820.207790.15815330.16116120.9730.9851000.171
2.782-3.0030.185770.15414140.15614910.9790.9851000.17
3.003-3.2870.185920.15812730.1613650.9750.9851000.178
3.287-3.670.171520.15511860.15512380.9840.9861000.174
3.67-4.2290.151600.13110210.13210810.9860.9891000.152
4.229-5.1580.159460.1349130.1359590.9860.9891000.147
5.158-7.2040.216500.1576710.167210.9730.9861000.178
7.204-32.4410.171270.2034130.2014400.9720.9771000.222

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