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Yorodumi- PDB-6ofr: The crystal structure of the outer membrane transporter YddB from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ofr | ||||||
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Title | The crystal structure of the outer membrane transporter YddB from Escherichia coli | ||||||
Components | TonB-dependent outer membrane receptor | ||||||
Keywords | TRANSPORT PROTEIN / Protein Transport / Gram-negative bacteria / Outer membrane / Nutrient Uptake / TonB-Dependent Transporter | ||||||
Function / homology | TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Porin protein / Uncharacterized protein YddB Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Grinter, R. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: PLoS Genet / Year: 2019 Title: Protease-associated import systems are widespread in Gram-negative bacteria. Authors: Rhys Grinter / Pok Man Leung / Lakshmi C Wijeyewickrema / Dene Littler / Simone Beckham / Robert N Pike / Daniel Walker / Chris Greening / Trevor Lithgow / Abstract: Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ...Bacteria have evolved sophisticated uptake machineries in order to obtain the nutrients required for growth. Gram-negative plant pathogens of the genus Pectobacterium obtain iron from the protein ferredoxin, which is produced by their plant hosts. This iron-piracy is mediated by the ferredoxin uptake system (Fus), a gene cluster encoding proteins that transport ferredoxin into the bacterial cell and process it proteolytically. In this work we show that gene clusters related to the Fus are widespread in bacterial species. Through structural and biochemical characterisation of the distantly related Fus homologues YddB and PqqL from Escherichia coli, we show that these proteins are analogous to components of the Fus from Pectobacterium. The membrane protein YddB shares common structural features with the outer membrane ferredoxin transporter FusA, including a large extracellular substrate binding site. PqqL is an active protease with an analogous periplasmic localisation and iron-dependent expression to the ferredoxin processing protease FusC. Structural analysis demonstrates that PqqL and FusC share specific features that distinguish them from other members of the M16 protease family. Taken together, these data provide evidence that protease associated import systems analogous to the Fus are widespread in Gram-negative bacteria. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ofr.cif.gz | 330.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ofr.ent.gz | 266.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ofr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/6ofr ftp://data.pdbj.org/pub/pdb/validation_reports/of/6ofr | HTTPS FTP |
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-Related structure data
Related structure data | 6ofsC 6oftC 4zgvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 86302.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yddB, ACU57_09575, BANRA_00721, BANRA_04049, BvCmsKSP026_02313, BvCmsSINP012_01435, C5N07_00015, CA593_20420, D0X26_01860, D3821_23605, DNQ41_11905, E4Z89_11620, E5M00_15980, EAI52_23140, ...Gene: yddB, ACU57_09575, BANRA_00721, BANRA_04049, BvCmsKSP026_02313, BvCmsSINP012_01435, C5N07_00015, CA593_20420, D0X26_01860, D3821_23605, DNQ41_11905, E4Z89_11620, E5M00_15980, EAI52_23140, EC3234A_33c00020, EC3426_02521, EPS71_22575, EXX71_23015, EYD11_11385, NCTC13462_06167, NCTC9037_02822, NCTC9045_02987, NCTC9062_00632, NCTC9073_01172, RK56_010145, SAMEA3753300_05217 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A024L3L4, UniProt: P31827*PLUS | ||||||||
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#2: Sugar | ChemComp-BOG / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.02 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.5 Details: 0.1 M Na cacodylate, 0.15 M Ca acetate, 15 % PEG 8000 and 20 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 11, 2015 / Details: Yes |
Radiation | Monochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.92 Å / Num. obs: 49176 / % possible obs: 99.6 % / Redundancy: 10.4 % / Biso Wilson estimate: 56.31 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.072 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.4→2.48 Å / Redundancy: 10.7 % / Rmerge(I) obs: 1.96 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4454 / CC1/2: 0.722 / Rpim(I) all: 0.622 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZGV Resolution: 2.4→47.92 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 2.4→47.92 Å
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