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- PDB-6i2j: Crystal structure of the ferric enterobactin receptor mutant (Q48... -

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Basic information

Entry
Database: PDB / ID: 6i2j
TitleCrystal structure of the ferric enterobactin receptor mutant (Q482A) 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 / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsMoynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
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
DepositionNov 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2019Provider: 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 1.2Jan 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 1.3Nov 13, 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)79,1533
Polymers78,4281
Non-polymers7252
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.964, 158.288, 78.474
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: 78428.078 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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 8000 ADA Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.96→79.14 Å / Num. obs: 21785 / % possible obs: 93.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 21.7
Reflection shellResolution: 2.96→3 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.627 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M9B

5m9b


Resolution: 2.96→79.14 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.867 / SU B: 63.656 / SU ML: 0.465 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31574 1024 5.1 %RANDOM
Rwork0.30109 ---
obs0.30187 18979 85.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 97.973 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å20 Å20 Å2
2--11.1 Å20 Å2
3----8.89 Å2
Refinement stepCycle: 1 / Resolution: 2.96→79.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 49 1 5416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195529
X-RAY DIFFRACTIONr_bond_other_d0.0010.024866
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9587505
X-RAY DIFFRACTIONr_angle_other_deg0.744311309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5845697
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.87324.307267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03715878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0651540
X-RAY DIFFRACTIONr_chiral_restr0.0910.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021144
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_it3.5435.2662791
X-RAY DIFFRACTIONr_mcbond_other3.5425.2662790
X-RAY DIFFRACTIONr_mcangle_it5.5237.8993487
X-RAY DIFFRACTIONr_mcangle_other5.5237.8993488
X-RAY DIFFRACTIONr_scbond_it3.4165.592738
X-RAY DIFFRACTIONr_scbond_other3.3785.5882737
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.298.2944019
X-RAY DIFFRACTIONr_long_range_B_refined9.99823146
X-RAY DIFFRACTIONr_long_range_B_other9.99923147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.956→3.033 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.51 82 -
Rwork0.379 1454 -
obs--90.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1198.238650.719644.598912.985811.389610.1025-2.36116.21921.7754-0.59351.62880.3296-0.53361.45660.73231.01030.4654-0.44381.3843-0.23971.917-82.313614.264580.7908
23.50090.0980.10231.79580.36676.08960.2117-0.1927-0.2841-0.481-0.0941-0.23280.1739-0.1384-0.11760.19440.00020.04760.0377-0.04810.3438-85.69527.631891.5707
31.52880.08810.59452.85750.35324.6448-0.0714-0.12850.1268-0.4934-0.16020.1291-0.3665-1.05130.23160.2780.1026-0.06580.2703-0.06030.4689-98.670334.338792.8765
41.64220.3893-1.26672.3648-0.978210.56820.164-0.17260.409-0.36650.0204-0.1913-1.04250.1572-0.18440.2261-0.05540.04360.0679-0.08520.4545-87.700339.658992.2686
57.85522.2484-5.25191.3463-2.301910.37640.3313-0.2810.6894-0.19390.09450.0962-0.92710.054-0.42570.3854-0.0373-0.03750.0943-0.14420.4838-88.978241.822996.1297
62.63970.6253-0.57132.09450.27196.78230.1906-0.19040.356-0.21090.12-0.2431-0.69990.2051-0.31060.2183-0.04340.06970.0352-0.09720.5081-80.032140.56897.1517
72.19050.47910.29552.04190.95513.80880.1728-0.4802-0.3796-0.12090.3068-0.61930.40550.8109-0.47950.22930.02010.00510.3337-0.05110.6173-72.292725.477399.7945
85.4993-0.23453.84752.22732.92877.77930.1620.4402-0.47910.125-0.0575-0.14060.82550.4077-0.10450.7905-0.12690.00490.20540.19580.5547-90.611911.863593.7136
92.8608-0.11460.23262.3567-0.17913.61930.1839-0.4474-0.4553-0.0197-0.18780.15880.6261-0.7650.00390.4316-0.2524-0.01410.27720.00320.4772-98.576619.482799.9603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 29
2X-RAY DIFFRACTION2A30 - 158
3X-RAY DIFFRACTION3A159 - 242
4X-RAY DIFFRACTION4A243 - 271
5X-RAY DIFFRACTION5A272 - 299
6X-RAY DIFFRACTION6A300 - 355
7X-RAY DIFFRACTION7A356 - 584
8X-RAY DIFFRACTION8A585 - 635
9X-RAY DIFFRACTION9A636 - 721

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