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Yorodumi- PDB-6brs: The Crystal Structure of the Ferredoxin Protease FusC in complex ... -
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-Basic information
Entry | Database: PDB / ID: 6brs | ||||||
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Title | The Crystal Structure of the Ferredoxin Protease FusC in complex with Arabidopsis Ferredoxin, Ethylmercury phosphate soaked dataset | ||||||
Components |
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Keywords | HYDROLASE / M16 Protease / Ferredoxin Binding / Ferredoxin Cleavage | ||||||
Function / homology | Function and homology information photosynthetic acclimation / photosynthetic electron transport chain / chloroplast / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / electron transfer activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Pectobacterium atrosepticum (bacteria) Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Grinter, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: PLoS Biol / Year: 2018 Title: FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants. Authors: Rhys Grinter / Iain D Hay / Jiangning Song / Jiawei Wang / Don Teng / Vijay Dhanesakaran / Jonathan J Wilksch / Mark R Davies / Dene Littler / Simone A Beckham / Ian R Henderson / Richard A ...Authors: Rhys Grinter / Iain D Hay / Jiangning Song / Jiawei Wang / Don Teng / Vijay Dhanesakaran / Jonathan J Wilksch / Mark R Davies / Dene Littler / Simone A Beckham / Ian R Henderson / Richard A Strugnell / Gordon Dougan / Trevor Lithgow / Abstract: Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the ...Iron is essential for life. Accessing iron from the environment can be a limiting factor that determines success in a given environmental niche. For bacteria, access of chelated iron from the environment is often mediated by TonB-dependent transporters (TBDTs), which are β-barrel proteins that form sophisticated channels in the outer membrane. Reports of iron-bearing proteins being used as a source of iron indicate specific protein import reactions across the bacterial outer membrane. The molecular mechanism by which a folded protein can be imported in this way had remained mysterious, as did the evolutionary process that could lead to such a protein import pathway. How does the bacterium evolve the specificity factors that would be required to select and import a protein encoded on another organism's genome? We describe here a model whereby the plant iron-bearing protein ferredoxin can be imported across the outer membrane of the plant pathogen Pectobacterium by means of a Brownian ratchet mechanism, thereby liberating iron into the bacterium to enable its growth in plant tissues. This import pathway is facilitated by FusC, a member of the same protein family as the mitochondrial processing peptidase (MPP). The Brownian ratchet depends on binding sites discovered in crystal structures of FusC that engage a linear segment of the plant protein ferredoxin. Sequence relationships suggest that the bacterial gene encoding FusC has previously unappreciated homologues in plants and that the protein import mechanism employed by the bacterium is an evolutionary echo of the protein import pathway in plant mitochondria and plastids. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6brs.cif.gz | 407.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6brs.ent.gz | 326.8 KB | Display | PDB format |
PDBx/mmJSON format | 6brs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6brs_validation.pdf.gz | 466.8 KB | Display | wwPDB validaton report |
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Full document | 6brs_full_validation.pdf.gz | 479.4 KB | Display | |
Data in XML | 6brs_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 6brs_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/6brs ftp://data.pdbj.org/pub/pdb/validation_reports/br/6brs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 3 molecules AFC
#1: Protein | Mass: 101378.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) (bacteria) Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA0879 / Production host: Escherichia coli (E. coli) / Strain (production host): C31 (DE3) / References: UniProt: Q6D8U3 |
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#2: Protein | Mass: 11342.354 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FD2, PETF, PETF1, At1g60950, T7P1.9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16972 |
-Protein/peptide , 1 types, 1 molecules E
#3: Protein/peptide | Mass: 358.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FD2, PETF, PETF1, At1g60950, T7P1.9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) |
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-Non-polymers , 3 types, 307 molecules
#4: Chemical | #5: Chemical | ChemComp-HG / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NaKPhos, 0.1 M Bistris Propane, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 30, 2017 / Details: Yes |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.62 Å / Num. obs: 61936 / % possible obs: 100 % / Redundancy: 29.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.26 / Rpim(I) all: 0.049 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 30.1 % / Rmerge(I) obs: 3.014 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4552 / CC1/2: 0.595 / Rpim(I) all: 0.788 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→41.645 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→41.645 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 10.618 Å / Origin y: 36.3151 Å / Origin z: 17.2147 Å
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Refinement TLS group | Selection details: all |