+Open data
-Basic information
Entry | Database: PDB / ID: 8oem | |||||||||
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Title | Crystal structure of FutA bound to Fe(II) | |||||||||
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 / outer membrane-bounded periplasmic space / metal ion binding / : / Putative iron ABC transporter, substrate binding protein Function and homology information | |||||||||
Biological species | Prochlorococcus marinus subsp. pastoris str. CCMP1986 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Bolton, R. / Tews, I. | |||||||||
Funding support | 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 | 8oem.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8oem.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 8oem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8oem_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8oem_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8oem_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 8oem_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/8oem ftp://data.pdbj.org/pub/pdb/validation_reports/oe/8oem | HTTPS FTP |
-Related structure data
Related structure data | 8c4yC 8oeiC 8oggC 8rk1C 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-FE2 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.72 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | |||||||||||||||||||||||||||
Detector | Type: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 16, 2018 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.7→47.5 Å / Num. obs: 30881 / % possible obs: 97.9 % / Redundancy: 65.4 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.009 / Rrim(I) all: 0.054 / Net I/σ(I): 71.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→47.5 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.752 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.095 Details: Hydrogens have been added in their riding positions
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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: 19.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→47.5 Å
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Refine LS restraints |
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LS refinement shell |
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