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

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Basic information

Entry
Database: PDB / ID: 6bpo
TitleThe crystal structure of the Ferric-Catecholate import receptor Fiu from K12 E. coli: Closed form (P1)
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 (TBDR) proteins profile. / TonB box, conserved site / TonB-dependent siderophore receptor / 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
Similarity search - Domain/homology
Catecholate siderophore receptor Fiu
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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.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
B: Catecholate siderophore receptor Fiu
C: Catecholate siderophore receptor Fiu
D: Catecholate siderophore receptor Fiu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)314,2476
Polymers313,6624
Non-polymers5852
Water4,612256
1
A: Catecholate siderophore receptor Fiu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7082
Polymers78,4151
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catecholate siderophore receptor Fiu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7082
Polymers78,4151
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catecholate siderophore receptor Fiu


Theoretical massNumber of molelcules
Total (without water)78,4151
Polymers78,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Catecholate siderophore receptor Fiu


Theoretical massNumber of molelcules
Total (without water)78,4151
Polymers78,4151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.674, 133.159, 135.100
Angle α, β, γ (deg.)101.50, 107.42, 92.88
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 78415.461 Da / Num. of mol.: 4
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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.99 Å3/Da / Density % sol: 69.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Bis-Tris Propane, 20 % PEG3350, 0.2 M Na-Malonate

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→50.31 Å / Num. obs: 116009 / % possible obs: 99 % / Observed criterion σ(I): 1.1 / Redundancy: 3.7 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.222 / Rpim(I) all: 0.151 / Net I/σ(I): 3.6
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.199 / Num. unique obs: 5714 / CC1/2: 0.491 / Rpim(I) all: 0.802 / % possible all: 98.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FP1
Resolution: 2.9→29.23 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.851 / SU R Cruickshank DPI: 0.509 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.448 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.301
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5866 5.06 %RANDOM
Rwork0.197 ---
obs0.199 115912 99 %-
Displacement parametersBiso mean: 56.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.6567 Å20.0872 Å22.8012 Å2
2---21.0498 Å2-5.8308 Å2
3---13.3932 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.9→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21644 0 40 256 21940
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00822253HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0930369HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7425SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes608HARMONIC2
X-RAY DIFFRACTIONt_gen_planes3296HARMONIC5
X-RAY DIFFRACTIONt_it22253HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion19.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3031SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact24235SEMIHARMONIC4
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2905 433 5.09 %
Rwork0.2282 8074 -
all0.2313 8507 -
obs--98.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9751-0.0515-0.29850.6482-0.25621.08160.0289-0.27970.11090.17870.04760.0685-0.11140.0193-0.0764-0.10030.03940.0371-0.0226-0.0591-0.2241110.722-98.3719113.1883
20.8514-0.0752-0.1530.54820.12510.85370.08450.11870.2273-0.05980.0361-0.0879-0.1660.0888-0.1207-0.1337-0.01520.0448-0.05430.0565-0.117866.8114-94.231860.1706
30.9021-0.09960.08460.6634-0.23020.780.05530.2433-0.1368-0.13510.00920.12720.1079-0.0709-0.0645-0.1497-0.0082-0.06610.0306-0.0789-0.1766118.9501-17.42846.7985
40.8402-0.18090.21830.4984-0.07311.4067-0.0013-0.168-0.20460.08720.09770.01480.20720.0401-0.0965-0.10480.0373-0.011-0.07440.0453-0.17175.3662-36.738396.1266
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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