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- PDB-6bpn: The crystal structure of the Ferric-Catecholate import receptor F... -

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Basic information

Entry
Database: PDB / ID: 6bpn
TitleThe crystal structure of the Ferric-Catecholate import receptor Fiu from E. coli K12: Open form (C2221)
ComponentsCatecholate siderophore receptor Fiu
KeywordsMEMBRANE PROTEIN / Ferric-Catecholate / TonB-Dependent Receptor / Membrane Transport / Antibiotic Uptake / Iron Transporter
Function / homology
Function and homology information


microcin transport / siderophore-dependent iron import into cell / siderophore uptake transmembrane transporter activity / siderophore transport / transmembrane transporter complex / cell outer membrane / signaling receptor activity / intracellular iron ion homeostasis / membrane
Similarity search - Function
TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily ...TonB-dependent receptor (TBDR) proteins signature 1. / TonB-dependent receptor, plug domain / TonB-dependent receptor (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor / TonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Chem-POG / Catecholate siderophore receptor Fiu
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGrinter, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106077/Z/14/Z United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2019
Title: The structure of the bacterial iron-catecholate transporter Fiu suggests that it imports substrates via a two-step mechanism.
Authors: Grinter, R. / Lithgow, T.
History
DepositionNov 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
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 / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catecholate siderophore receptor Fiu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5999
Polymers78,4151
Non-polymers2,1848
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-12 kcal/mol
Surface area28500 Å2
Unit cell
Length a, b, c (Å)107.927, 148.945, 105.061
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1249-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Catecholate siderophore receptor Fiu / Ferric iron uptake protein / TonB-dependent receptor Fiu


Mass: 78415.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fiu, ybiL, b0805, JW0790 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: P75780
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 415 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical
ChemComp-POG / (20S)-2,5,8,11,14,17-HEXAMETHYL-3,6,9,12,15,18-HEXAOXAHENICOSANE-1,20-DIOL / POLYPROPYLENE GLYCOL / HEPTAPROPYLENE GLYCOL / Polypropylene glycol


Mass: 424.569 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H44O8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 1.0 M LiCl, 0.1 M Citrate, 20 % PEG 6000, 4% Polypropylene glycol P400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2017
RadiationMonochromator: Silicin / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→48 Å / Num. obs: 49686 / % possible obs: 100 % / Observed criterion σ(I): 2.4 / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.082 / Net I/σ(I): 10.5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4026 / CC1/2: 0.881 / Rpim(I) all: 0.486 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FP1

5fp1


Resolution: 2.1→48 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.6
RfactorNum. reflection% reflection
Rfree0.2201 2471 4.98 %
Rwork0.1748 --
obs0.177 49647 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 146 408 5563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075276
X-RAY DIFFRACTIONf_angle_d0.8177170
X-RAY DIFFRACTIONf_dihedral_angle_d11.7913038
X-RAY DIFFRACTIONf_chiral_restr0.052814
X-RAY DIFFRACTIONf_plane_restr0.005921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14040.30261190.21922630X-RAY DIFFRACTION100
2.1404-2.18410.24921300.20222607X-RAY DIFFRACTION100
2.1841-2.23160.2471420.19472547X-RAY DIFFRACTION100
2.2316-2.28350.27911360.19092601X-RAY DIFFRACTION100
2.2835-2.34060.24491460.18252570X-RAY DIFFRACTION100
2.3406-2.40390.23411300.18732623X-RAY DIFFRACTION100
2.4039-2.47460.21511310.1752585X-RAY DIFFRACTION100
2.4746-2.55450.2151180.16532649X-RAY DIFFRACTION100
2.5545-2.64580.21571320.16292584X-RAY DIFFRACTION100
2.6458-2.75170.22081400.1612593X-RAY DIFFRACTION100
2.7517-2.87690.22081540.16352607X-RAY DIFFRACTION100
2.8769-3.02860.2151620.16292583X-RAY DIFFRACTION100
3.0286-3.21830.22271490.16142600X-RAY DIFFRACTION100
3.2183-3.46670.18121300.15172640X-RAY DIFFRACTION100
3.4667-3.81540.20681370.1522640X-RAY DIFFRACTION100
3.8154-4.36720.17811380.16532665X-RAY DIFFRACTION100
4.3672-5.5010.20221280.16852674X-RAY DIFFRACTION100
5.501-48.01420.26481490.23012778X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 23.5118 Å / Origin y: 49.1798 Å / Origin z: 27.6746 Å
111213212223313233
T0.1414 Å2-0.0025 Å2-0.008 Å2-0.1523 Å20.0061 Å2--0.1527 Å2
L0.1707 °2-0.1682 °2-0.0737 °2-0.6055 °20.3777 °2--0.4557 °2
S0.0342 Å °0.0055 Å °0.0072 Å °-0.0571 Å °0.007 Å °-0.0764 Å °-0.0429 Å °0.0381 Å °-0.0388 Å °
Refinement TLS groupSelection details: all

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