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- PDB-6z8a: Outer membrane FoxA in complex with nocardamine -

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Basic information

Entry
Database: PDB / ID: 6z8a
TitleOuter membrane FoxA in complex with nocardamine
ComponentsFerrioxamine receptor FoxA
KeywordsMEMBRANE PROTEIN / TonB-dependent transporter Outer membrane transporter Siderophore uptake transporter
Function / homology
Function and homology information


siderophore transport / siderophore uptake transmembrane transporter activity / 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 / TonB-dependent receptor (TBDR) proteins profile. / Vitamin B12 transporter BtuB-like / TonB-dependent receptor-like, beta-barrel / TonB dependent receptor-like, beta-barrel / 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
Chem-6L0 / : / Ferrioxamine receptor FoxA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsJosts, I. / Tidow, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Nocardamine-Dependent Iron Uptake in Pseudomonas aeruginosa : Exclusive Involvement of the FoxA Outer Membrane Transporter.
Authors: Normant, V. / Josts, I. / Kuhn, L. / Perraud, Q. / Fritsch, S. / Hammann, P. / Mislin, G.L.A. / Tidow, H. / Schalk, I.J.
History
DepositionJun 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferrioxamine receptor FoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6077
Polymers85,5861
Non-polymers1,0216
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-61 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.222, 95.222, 178.651
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 , 1 types, 1 molecules A

#1: Protein Ferrioxamine receptor FoxA


Mass: 85585.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: foxA, PA2466 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I116

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Non-polymers , 5 types, 14 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-6L0 / (8E)-6,17,28-trihydroxy-1,6,12,17,23,28-hexaazacyclotritriacont-8-ene-2,5,13,16,24,27-hexone


Mass: 598.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46N6O9 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.8M Ammonium sulfate, 0.1M HEPES, 0.3% octyl glucopyranoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→82.465 Å / Num. obs: 14984 / % possible obs: 94 % / Redundancy: 20 % / CC1/2: 0.99 / Rmerge(I) obs: 0.18 / Rrim(I) all: 0.185 / Net I/σ(I): 12.8
Reflection shellResolution: 2.95→3.1 Å / Rmerge(I) obs: 2.58 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 750 / CC1/2: 0.697 / % possible all: 99

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I98

6i98


Resolution: 2.95→82.46 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.816 / SU B: 41.287 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 709 4.7 %RANDOM
Rwork0.2348 ---
obs0.2365 14274 73.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 135.88 Å2 / Biso mean: 64.968 Å2 / Biso min: 39.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2.95→82.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5325 0 62 8 5395
Biso mean--72.79 55.18 -
Num. residues----677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135509
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174815
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.6537471
X-RAY DIFFRACTIONr_angle_other_deg1.4341.59511183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3785676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59122.571315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.52615858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.961535
X-RAY DIFFRACTIONr_chiral_restr0.1560.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026288
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021221
LS refinement shellResolution: 2.951→3.027 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 17 -
Rwork0.343 388 -
all-405 -
obs--27.22 %
Refinement TLS params.Method: refined / Origin x: -35.8652 Å / Origin y: 5.2978 Å / Origin z: -11.5532 Å
111213212223313233
T0.1532 Å2-0.009 Å20.016 Å2-0.0539 Å2-0.0109 Å2--0.0649 Å2
L1.3583 °20.3834 °2-0.8124 °2-1.7902 °2-0.4686 °2--1.7514 °2
S-0.0921 Å °0.1638 Å °-0.2576 Å °-0.0303 Å °-0.1189 Å °-0.2301 Å °0.2161 Å °0.0647 Å °0.211 Å °

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