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Yorodumi- PDB-8rk1: Crystal structure of FutA bound to Fe(III) solved by neutron diff... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8rk1 | |||||||||
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Title | Crystal structure of FutA bound to Fe(III) solved by neutron diffraction | |||||||||
Components | Putative iron ABC transporter, substrate binding protein | |||||||||
Keywords | METAL BINDING PROTEIN / Periplasmic iron-binding protein / metal ion binding / iron homeostasis | |||||||||
Function / homology | Bacterial extracellular solute-binding protein / Ferric binding protein / iron ion transport / metal ion binding / : / Putative iron ABC transporter, substrate binding protein Function and homology information | |||||||||
Biological species | Prochlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria) | |||||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.095 Å | |||||||||
Authors | Bolton, R. / Tews, I. | |||||||||
Funding support | United Kingdom, 2items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rk1.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8rk1.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 8rk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/8rk1 ftp://data.pdbj.org/pub/pdb/validation_reports/rk/8rk1 | HTTPS FTP |
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-Related structure data
Related structure data | 8c4yC 8oeiC 8oemC 8oggC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: 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 |
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#2: Chemical | ChemComp-FE / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.22 % |
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Crystal grow | Temperature: 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. |
-Data collection
Diffraction | Mean temperature: 294 K / Serial crystal experiment: N |
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Diffraction source | Source: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 3.1 Å |
Detector | Type: BIODIFF / Detector: IMAGE PLATE / Date: Feb 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 3.1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Refinement | Method 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.465 Å2
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Refine LS restraints |
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LS refinement shell | Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 20
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