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- PDB-8s34: Ferric-mycobactin receptor (FemA) in complex with aeruginic acid -

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Basic information

Entry
Database: PDB / ID: 8s34
TitleFerric-mycobactin receptor (FemA) in complex with aeruginic acid
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
: / : / : / pentane-2,4-dione / Ferric-mycobactin receptor, FemA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
DepositionFeb 19, 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

Downloads & links

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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)172,17234
Polymers168,0972
Non-polymers4,07532
Water10,881604
1
B: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,16916
Polymers84,0481
Non-polymers2,12115
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ferric-mycobactin receptor, FemA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,00318
Polymers84,0481
Non-polymers1,95517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.857, 84.878, 86.855
Angle α, β, γ (deg.)90.008, 118.530, 113.699
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules BA

#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

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Non-polymers , 7 types, 636 molecules

#2: 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
#3: Chemical
ChemComp-A1H49 / 2-(2-hydroxyphenyl)-1,3-thiazole-4-carboxylic acid


Mass: 221.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H7NO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-P2D / pentane-2,4-dione


Mass: 100.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O2
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: Peg 400, Hepes

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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 X 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.86→75.47 Å / Num. obs: 149305 / % possible obs: 94.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 28.01 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.128 / Net I/σ(I): 9.7
Reflection shellResolution: 1.86→1.89 Å / Num. unique obs: 4881 / CC1/2: 0.282

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→75.47 Å / SU ML: 0.2763 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.3026 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 7174 4.82 %
Rwork0.2135 141745 -
obs0.2151 148919 94.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.5 Å2
Refinement stepCycle: LAST / Resolution: 1.86→75.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10330 0 202 604 11136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007110786
X-RAY DIFFRACTIONf_angle_d0.944214619
X-RAY DIFFRACTIONf_chiral_restr0.05431569
X-RAY DIFFRACTIONf_plane_restr0.00581957
X-RAY DIFFRACTIONf_dihedral_angle_d8.9778726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.40681760.37752886X-RAY DIFFRACTION58.49
1.88-1.90.37871910.36263310X-RAY DIFFRACTION66.33
1.9-1.920.3992070.35223730X-RAY DIFFRACTION74.98
1.92-1.950.38762230.33914368X-RAY DIFFRACTION87.33
1.95-1.970.35332440.3144778X-RAY DIFFRACTION94.74
1.97-20.33842290.29554789X-RAY DIFFRACTION96.13
2-2.030.31392520.27784883X-RAY DIFFRACTION96.8
2.03-2.060.28482640.26444797X-RAY DIFFRACTION96.77
2.06-2.090.29382450.26144858X-RAY DIFFRACTION96.94
2.09-2.130.29062700.26044873X-RAY DIFFRACTION97.22
2.13-2.160.3072590.25064833X-RAY DIFFRACTION97.31
2.16-2.20.26942460.23744867X-RAY DIFFRACTION97.3
2.2-2.240.27722310.23364950X-RAY DIFFRACTION97.57
2.24-2.290.25612760.22724839X-RAY DIFFRACTION97.45
2.29-2.340.25682680.22674829X-RAY DIFFRACTION97.66
2.34-2.390.26792610.21424879X-RAY DIFFRACTION97.74
2.39-2.450.26822280.2164909X-RAY DIFFRACTION97.96
2.45-2.520.2692290.21134925X-RAY DIFFRACTION97.8
2.52-2.60.24542520.2034924X-RAY DIFFRACTION98.18
2.6-2.680.23062360.19954910X-RAY DIFFRACTION98.21
2.68-2.770.2582550.19214947X-RAY DIFFRACTION98.23
2.77-2.890.22452700.18864917X-RAY DIFFRACTION98.11
2.89-3.020.23922250.20154930X-RAY DIFFRACTION98.57
3.02-3.180.23222600.20174932X-RAY DIFFRACTION98.63
3.18-3.380.22932630.20284935X-RAY DIFFRACTION98.69
3.38-3.640.22312690.19714922X-RAY DIFFRACTION98.8
3.64-40.23392420.19424973X-RAY DIFFRACTION99.05
4-4.580.21492410.18534987X-RAY DIFFRACTION99.18
4.58-5.770.21961350.18865081X-RAY DIFFRACTION99.28
5.77-75.470.20992270.20574984X-RAY DIFFRACTION99.09

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