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- PDB-6r1f: Crystal structure of the ferric enterobactin receptor mutant R480... -

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Basic information

Entry
Database: PDB / ID: 6r1f
TitleCrystal structure of the ferric enterobactin receptor mutant R480A from Pseudomonas aeruginosa (PfeA) in complex with enterobactin
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor / protochelin
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 siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / 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 siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / 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
Chem-EB4 / : / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative115525 United Kingdom
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
DepositionMar 14, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionApr 10, 2019ID: 6I2L
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 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 1.3Jan 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric enterobactin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1243
Polymers78,3991
Non-polymers7252
Water181
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.500, 157.260, 78.000
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: 78399.008 Da / Num. of mol.: 1
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: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin


Mass: 669.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H27N3O15
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.48 Å3/Da / Density % sol: 64.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion / Details: PEG 8000 ADA Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.11→43.51 Å / Num. obs: 19766 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Net I/σ(I): 14.2
Reflection shellResolution: 3.11→3.16 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 968 / CC1/2: 0.52 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q5E

6q5e


Resolution: 3.11→43.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.927 / SU B: 54.711 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25644 996 5 %RANDOM
Rwork0.21189 ---
obs0.21413 18734 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 126.632 Å2
Baniso -1Baniso -2Baniso -3
1-8.67 Å20 Å20 Å2
2---2.39 Å20 Å2
3----6.28 Å2
Refinement stepCycle: LAST / Resolution: 3.11→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5364 0 49 1 5414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135533
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174863
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.6477503
X-RAY DIFFRACTIONr_angle_other_deg1.1571.57811300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4055697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31422.427309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23715877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9081539
X-RAY DIFFRACTIONr_chiral_restr0.0520.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026393
X-RAY DIFFRACTIONr_gen_planes_other00.021176
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_it5.4399.4242791
X-RAY DIFFRACTIONr_mcbond_other5.4399.4242790
X-RAY DIFFRACTIONr_mcangle_it7.96214.1613487
X-RAY DIFFRACTIONr_mcangle_other7.96114.1623488
X-RAY DIFFRACTIONr_scbond_it5.97910.0192742
X-RAY DIFFRACTIONr_scbond_other5.97910.0192741
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.96814.8364017
X-RAY DIFFRACTIONr_long_range_B_refined10.85611429
X-RAY DIFFRACTIONr_long_range_B_other10.85511430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.11→3.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 68 -
Rwork0.387 1347 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -83.9249 Å / Origin y: 27.0181 Å / Origin z: 95.7734 Å
111213212223313233
T0.0465 Å2-0.0253 Å20.0189 Å2-0.0462 Å2-0.0454 Å2--0.1556 Å2
L1.7311 °20.2955 °20.217 °2-4.3179 °21.1753 °2--4.4556 °2
S-0.011 Å °-0.1968 Å °0.0098 Å °-0.1783 Å °0.0568 Å °-0.2998 Å °-0.4464 Å °0.2053 Å °-0.0458 Å °

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