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- PDB-6ofr: The crystal structure of the outer membrane transporter YddB from... -

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Basic information

Entry
Database: PDB / ID: 6ofr
TitleThe crystal structure of the outer membrane transporter YddB from Escherichia coli
ComponentsTonB-dependent outer membrane receptor
KeywordsTRANSPORT PROTEIN / Protein Transport / Gram-negative bacteria / Outer membrane / Nutrient Uptake / TonB-Dependent Transporter
Function / homologyTonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / cell outer membrane / TonB-dependent receptor / Uncharacterized protein YddB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGrinter, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106077/Z/14/Z United Kingdom
CitationJournal: 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
DepositionApr 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TonB-dependent outer membrane receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,67413
Polymers86,3031
Non-polymers2,37112
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.520, 76.520, 412.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TonB-dependent outer membrane receptor / TonB-dependent Receptor Plug Domain protein / TonB-dependent outer membrane receptor / TonB-dependent receptor


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
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.1 M Na cacodylate, 0.15 M Ca acetate, 15 % PEG 8000 and 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 11, 2015 / Details: Yes
RadiationMonochromator: Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZGV

4zgv


Resolution: 2.4→47.92 Å / Cross valid method: FREE R-VALUE /
Num. reflection% reflection
obs49176 99.9 %
Refinement stepCycle: LAST / Resolution: 2.4→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6062 0 160 244 6466

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