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- PDB-9f2t: Ferric-mycobactin receptor (FemA) -

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Basic information

Entry
Database: PDB / ID: 9f2t
TitleFerric-mycobactin receptor (FemA)
ComponentsFerric-mycobactin receptor, FemA
KeywordsMEMBRANE PROTEIN / 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
ACETATE ION / Ferric-mycobactin receptor, FemA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionApr 24, 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
B: Ferric-mycobactin receptor, FemA
A: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,60515
Polymers168,0972
Non-polymers2,50813
Water8,683482
1
B: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3957
Polymers84,0481
Non-polymers1,3476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2108
Polymers84,0481
Non-polymers1,1627
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.678, 84.954, 86.702
Angle α, β, γ (deg.)89.966, 61.596, 66.264
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Ferric-mycobactin receptor, FemA


Mass: 84048.414 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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG 400, calcium acetate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2.05→75.55 Å / Num. obs: 115401 / % possible obs: 98.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.76 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.201 / Net I/σ(I): 7.1
Reflection shellResolution: 2.05→2.08 Å / Rmerge(I) obs: 1.33 / Num. unique obs: 5668 / CC1/2: 0.325

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→75.55 Å / SU ML: 0.2973 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8409 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2706 4627 4.96 %
Rwork0.2252 88597 -
obs0.2274 93224 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→75.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10282 0 133 482 10897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007510614
X-RAY DIFFRACTIONf_angle_d0.919114368
X-RAY DIFFRACTIONf_chiral_restr0.05381552
X-RAY DIFFRACTIONf_plane_restr0.00591917
X-RAY DIFFRACTIONf_dihedral_angle_d9.51786321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.30981580.27852920X-RAY DIFFRACTION97.44
2.23-2.250.34331520.27892927X-RAY DIFFRACTION97.41
2.25-2.280.2951460.25562944X-RAY DIFFRACTION97.45
2.28-2.310.28471530.25012913X-RAY DIFFRACTION97.58
2.31-2.340.27841330.2432969X-RAY DIFFRACTION97.67
2.34-2.370.30781620.24562886X-RAY DIFFRACTION97.44
2.37-2.40.31511640.25062964X-RAY DIFFRACTION97.93
2.4-2.440.33011800.2582900X-RAY DIFFRACTION97.62
2.44-2.480.37251430.26422984X-RAY DIFFRACTION97.93
2.48-2.520.28221600.25982877X-RAY DIFFRACTION97.87
2.52-2.560.28051090.24783030X-RAY DIFFRACTION97.97
2.56-2.610.28971710.23452919X-RAY DIFFRACTION98.22
2.61-2.660.32851560.23642952X-RAY DIFFRACTION97.86
2.66-2.710.30361770.22932933X-RAY DIFFRACTION98.36
2.71-2.770.28061570.23122922X-RAY DIFFRACTION97.96
2.77-2.840.25221770.22212916X-RAY DIFFRACTION97.97
2.84-2.910.29171810.22642960X-RAY DIFFRACTION98.56
2.91-2.990.27251670.23182958X-RAY DIFFRACTION98.61
2.99-3.070.30041530.22882951X-RAY DIFFRACTION98.6
3.07-3.170.30471380.22622961X-RAY DIFFRACTION98.6
3.17-3.290.2521070.23193037X-RAY DIFFRACTION98.74
3.29-3.420.28891620.22222946X-RAY DIFFRACTION98.73
3.42-3.570.2311760.21912953X-RAY DIFFRACTION98.86
3.57-3.760.26831330.21312975X-RAY DIFFRACTION99.01
3.76-40.26481700.21762977X-RAY DIFFRACTION99.09
4-4.310.23661640.20532960X-RAY DIFFRACTION99.08
4.31-4.740.22781440.18952990X-RAY DIFFRACTION98.96
4.74-5.420.23421500.20892996X-RAY DIFFRACTION99.34
5.42-6.830.24741310.21722999X-RAY DIFFRACTION99.55
6.83-75.550.25371530.2192978X-RAY DIFFRACTION98.61

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