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- PDB-5out: CRYSTAL STRUCTURE OF THE FERRIC ENTEROBACTIN RECEPTOR (PFEA) MUTA... -

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Basic information

Entry
Database: PDB / ID: 5out
TitleCRYSTAL STRUCTURE OF THE FERRIC ENTEROBACTIN RECEPTOR (PFEA) MUTANT (G324V) FROM PSEUDOMONAS AERUGINOSA
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / TBDT
Function / homology
Function and homology information


colicin transmembrane transporter activity / siderophore transmembrane transport / siderophore transport / siderophore uptake transmembrane transporter activity / enterobactin transport / enterobactin transmembrane transporter activity / outer membrane / enterobactin binding / cell outer membrane / signaling receptor activity
Similarity search - Function
TonB-dependent receptor, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / Maltoporin; Chain A / 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, beta-barrel domain / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / TonB-dependent siderophore receptor / Maltoporin; Chain A / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsMoynie, L. / Naismith, J.H.
CitationJournal: Nat Commun / Year: 2019
Title: The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model.
Authors: Moynie, L. / Milenkovic, S. / Mislin, G.L.A. / Gasser, V. / Malloci, G. / Baco, E. / McCaughan, R.P. / Page, M.G.P. / Schalk, I.J. / Ceccarelli, M. / Naismith, J.H.
History
DepositionAug 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Ferric enterobactin receptor


Theoretical massNumber of molelcules
Total (without water)78,5271
Polymers78,5271
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.680, 158.130, 77.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ferric enterobactin receptor


Mass: 78527.203 Da / Num. of mol.: 1 / Mutation: G324V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pfeA, PA2688 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05098
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.44 Å3/Da / Density % sol: 64.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG 8000 ADA Magnesium acetate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→39.08 Å / Num. obs: 19876 / % possible obs: 80.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.7
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.377 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.669 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.9→39.08 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.88 / SU B: 57.47 / SU ML: 0.423 / Cross valid method: THROUGHOUT / ESU R Free: 0.505 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29651 984 5 %RANDOM
Rwork0.25307 ---
obs0.2552 18869 80.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 69.496 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--7.19 Å2-0 Å2
3----5.42 Å2
Refinement stepCycle: 1 / Resolution: 2.9→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5438 0 0 7 5445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195550
X-RAY DIFFRACTIONr_bond_other_d0.0020.024910
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9477533
X-RAY DIFFRACTIONr_angle_other_deg0.896311413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02424.391271
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53315891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0131540
X-RAY DIFFRACTIONr_chiral_restr0.0740.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216370
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021138
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2093.4682827
X-RAY DIFFRACTIONr_mcbond_other0.2093.4682826
X-RAY DIFFRACTIONr_mcangle_it0.3465.2023532
X-RAY DIFFRACTIONr_mcangle_other0.3465.2023533
X-RAY DIFFRACTIONr_scbond_it0.1693.4732723
X-RAY DIFFRACTIONr_scbond_other0.1693.4732723
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.2875.2074000
X-RAY DIFFRACTIONr_long_range_B_refined0.70938.7565728
X-RAY DIFFRACTIONr_long_range_B_other0.70938.7585729
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 70 -
Rwork0.397 1399 -
obs--82.11 %
Refinement TLS params.Method: refined / Origin x: -2.6818 Å / Origin y: 27.5619 Å / Origin z: -17.3626 Å
111213212223313233
T0.1517 Å20.0277 Å20.0541 Å2-0.0376 Å20.0494 Å2--0.2963 Å2
L1.3622 °2-0.3181 °20.0029 °2-2.3362 °2-0.9778 °2--3.8019 °2
S0.0362 Å °0.1513 Å °-0.0208 Å °0.5598 Å °0.083 Å °0.17 Å °-0.1254 Å °-0.1837 Å °-0.1191 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 151
2X-RAY DIFFRACTION1A152 - 183
3X-RAY DIFFRACTION1A184 - 239
4X-RAY DIFFRACTION1A240 - 293
5X-RAY DIFFRACTION1A294 - 353
6X-RAY DIFFRACTION1A354 - 435
7X-RAY DIFFRACTION1A436 - 560
8X-RAY DIFFRACTION1A561 - 607
9X-RAY DIFFRACTION1A608 - 721

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