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- PDB-9fvq: Ferric-mycobactin receptor (FemA) in complex with pyochelin -

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Basic information

Entry
Database: PDB / ID: 9fvq
TitleFerric-mycobactin receptor (FemA) in complex with pyochelin
ComponentsFerric-mycobactin receptor, FemA
KeywordsMEMBRANE PROTEIN / Pyochelin / TonB dependent transporter
Function / homology
Function and homology information


siderophore-iron import into cell / siderophore transport / siderophore uptake transmembrane transporter activity / sigma factor activity / cell outer membrane / regulation of iron ion transport / signaling receptor activity / cytosol
Similarity search - Function
Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like ...Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / TonB-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
Similarity search - Domain/homology
PYOCHELIN FE(III) / : / : / pentane-2,4-dione / Ferric-mycobactin receptor, FemA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.031 Å
AuthorsMoynie, L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Structure of the Outer Membrane Transporter FemA and Its Role in the Uptake of Ferric Dihydro-Aeruginoic Acid and Ferric Aeruginoic Acid in Pseudomonas aeruginosa .
Authors: Will, V. / Moynie, L. / Si Ahmed Charrier, E. / Le Bas, A. / Kuhn, L. / Volck, F. / Chicher, J. / Aksoy, H. / Madec, M. / Antheaume, C. / Mislin, G.L.A. / Schalk, I.J.
History
DepositionJun 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric-mycobactin receptor, FemA
B: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,74458
Polymers145,8122
Non-polymers6,93256
Water13,331740
1
A: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,39130
Polymers72,9061
Non-polymers3,48529
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,35228
Polymers72,9061
Non-polymers3,44627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.836, 84.662, 86.965
Angle α, β, γ (deg.)89.959, 118.666, 113.585
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferric-mycobactin receptor, FemA


Mass: 72905.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: femA, PA1910 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I2J4

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Non-polymers , 8 types, 796 molecules

#2: Chemical ChemComp-188 / PYOCHELIN FE(III)


Mass: 378.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14FeN2O3S2
#3: Chemical ChemComp-A1IG8 / Pyochelin Fe(III) isomer / (2R,4R)-2-[(4S)-2-(2-hydroxyphenyl)-4,5-dihydro-1,3-thiazol-4-yl]-3-methyl-1,3-thiazolidine-4-carboxylic acid / iron


Mass: 378.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14FeN2O3S2
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-P2D / pentane-2,4-dione


Mass: 100.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.31 Å3/Da / Density % sol: 62.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 4000, Magnesium acetate MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.03→66.72 Å / Num. obs: 116549 / % possible obs: 96.64 % / Redundancy: 3.36 % / CC1/2: 0.982 / Rmerge(I) obs: 0.149 / Net I/σ(I): 9.3
Reflection shellResolution: 2.03→2.07 Å / Num. unique obs: 4548 / CC1/2: 0.721 / % possible all: 74.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.031→66.72 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.885 / SU ML: 0.105 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2232 2007 1.723 %
Rwork0.1821 114469 -
all0.183 --
obs-116476 96.58 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.987 Å2-0.028 Å20.439 Å2
2--0.16 Å2-0.441 Å2
3----0.663 Å2
Refinement stepCycle: LAST / Resolution: 2.031→66.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10284 0 333 740 11357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01210962
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610207
X-RAY DIFFRACTIONr_angle_refined_deg2.2731.82714711
X-RAY DIFFRACTIONr_angle_other_deg0.7521.74923405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85851362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.085.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.394101649
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6510517
X-RAY DIFFRACTIONr_chiral_restr0.1090.21585
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213302
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022658
X-RAY DIFFRACTIONr_nbd_refined0.2090.21892
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.29651
X-RAY DIFFRACTIONr_nbtor_refined0.1830.24966
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.26398
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2857
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.218
X-RAY DIFFRACTIONr_nbd_other0.2190.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.214
X-RAY DIFFRACTIONr_mcbond_it2.62.075412
X-RAY DIFFRACTIONr_mcbond_other2.5992.075412
X-RAY DIFFRACTIONr_mcangle_it3.5623.7036780
X-RAY DIFFRACTIONr_mcangle_other3.5623.7036781
X-RAY DIFFRACTIONr_scbond_it4.7172.4965550
X-RAY DIFFRACTIONr_scbond_other4.3452.4845522
X-RAY DIFFRACTIONr_scangle_it5.3744.3477929
X-RAY DIFFRACTIONr_scangle_other5.3744.3487930
X-RAY DIFFRACTIONr_lrange_it7.46222.54611685
X-RAY DIFFRACTIONr_lrange_other7.38822.30311486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.031-2.0830.2681200.2256857X-RAY DIFFRACTION78.2789
2.083-2.140.2631440.2238227X-RAY DIFFRACTION96.1631
2.14-2.2020.251480.2128072X-RAY DIFFRACTION97.2436
2.202-2.270.2411560.1957826X-RAY DIFFRACTION97.2466
2.27-2.3440.2191510.1787634X-RAY DIFFRACTION97.4099
2.344-2.4270.2421190.1677403X-RAY DIFFRACTION97.6249
2.427-2.5180.2021190.1677072X-RAY DIFFRACTION97.8634
2.518-2.6210.2091090.1646902X-RAY DIFFRACTION97.7824
2.621-2.7370.1911020.1596612X-RAY DIFFRACTION98.1579
2.737-2.870.2261100.1696335X-RAY DIFFRACTION98.1273
2.87-3.0250.2371010.1746037X-RAY DIFFRACTION98.3811
3.025-3.2090.2161030.1665703X-RAY DIFFRACTION98.6241
3.209-3.4290.2081030.1695350X-RAY DIFFRACTION98.7147
3.429-3.7030.225980.185017X-RAY DIFFRACTION98.917
3.703-4.0560.205830.1854609X-RAY DIFFRACTION99.1128
4.056-4.5320.219780.1684171X-RAY DIFFRACTION99.1136
4.532-5.2290.206630.1663710X-RAY DIFFRACTION99.3679
5.229-6.3950.255540.2093135X-RAY DIFFRACTION99.5318
6.395-9.0030.242340.1972427X-RAY DIFFRACTION99.7164
9.003-66.720.149120.2891370X-RAY DIFFRACTION99.7834

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