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- PDB-6i96: Structure of the ferrioxamine B transporter FoxA from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 6i96
TitleStructure of the ferrioxamine B transporter FoxA from Pseudomonas aeruginosa in complex with ferrioxamine B
ComponentsFerric hydroxamate uptake
KeywordsMEMBRANE PROTEIN / outer membrane iron
Function / homology
Function and homology information


siderophore-iron transmembrane transporter activity / siderophore uptake transmembrane transporter activity / siderophore transport / outer membrane / cell outer membrane / signaling receptor activity / cell surface receptor signaling pathway
Similarity search - Function
Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / 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
Ferrioxamine B / Ferrichrome-iron receptor / Ferrioxamine receptor FoxA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJosts, I. / Tidow, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Elife / Year: 2019
Title: Ternary structure of the outer membrane transporter FoxA with resolved signalling domain provides insights into TonB-mediated siderophore uptake.
Authors: Josts, I. / Veith, K. / Tidow, H.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric hydroxamate uptake
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,18529
Polymers75,4221
Non-polymers5,76428
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8980 Å2
ΔGint-24 kcal/mol
Surface area26370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.890, 94.890, 177.612
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 14 molecules A

#1: Protein Ferric hydroxamate uptake / Ferrichrome-iron receptor / Ferrioxamine receptor FoxA / TonB-dependent siderophore receptor


Mass: 75421.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: fhuA, fhuA_5, C0044_18480, CAZ10_13360, CCBH4851_00003, DZ940_30305, EGY23_22030, PAERUG_E15_London_28_01_14_03466
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0C7CQY7, UniProt: Q9I116*PLUS
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-0UE / Ferrioxamine B


Mass: 613.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H45FeN6O8
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.8M Ammonium sulfate, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→82.18 Å / Num. obs: 79352 / % possible obs: 99.2 % / Redundancy: 17 % / CC1/2: 0.988 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.051 / Rrim(I) all: 0.156 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.288 / Mean I/σ(I) obs: 1 / Num. unique obs: 4129 / CC1/2: 0.279 / Rrim(I) all: 1.449 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→82.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.256 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.116
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 3949 5 %RANDOM
Rwork0.1811 ---
obs0.183 75099 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.87 Å2 / Biso mean: 48.723 Å2 / Biso min: 26.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.63 Å20 Å2
2--1.26 Å20 Å2
3----4.1 Å2
Refinement stepCycle: final / Resolution: 1.85→82.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 363 257 5945
Biso mean--81.76 47.78 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0195803
X-RAY DIFFRACTIONr_bond_other_d0.0030.025179
X-RAY DIFFRACTIONr_angle_refined_deg3.1832.0037833
X-RAY DIFFRACTIONr_angle_other_deg1.352312091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3145676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13424.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.18615858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1661535
X-RAY DIFFRACTIONr_chiral_restr0.1970.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026259
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021188
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 278 -
Rwork0.409 5174 -
all-5452 -
obs--92.93 %
Refinement TLS params.Method: refined / Origin x: -13.267 Å / Origin y: 33.4176 Å / Origin z: 18.1903 Å
111213212223313233
T0.0418 Å2-0.024 Å20.0101 Å2-0.1306 Å2-0.0232 Å2--0.0397 Å2
L0.9106 °2-0.0083 °2-0.5246 °2-0.3533 °20.0427 °2--1.0833 °2
S-0.0674 Å °0.0237 Å °-0.1395 Å °-0.0495 Å °-0.0743 Å °0.0729 Å °0.1588 Å °-0.0211 Å °0.1417 Å °

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