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- PDB-5nr2: Crystal structure of the ferric enterobactin receptor (PfeA) from... -

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Basic information

Entry
Database: PDB / ID: 5nr2
TitleCrystal structure of the ferric enterobactin receptor (PfeA) from Pseudomonas aeruginosa in complex with azotochelin
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor / azotochelin
Function / homology
Function and homology information


siderophore transport / colicin transmembrane transporter activity / siderophore transmembrane 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 siderophore receptor / TonB-dependent receptor, conserved site / TonB-dependent receptor (TBDR) proteins signature 2. / 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
Similarity search - Domain/homology
Azotochelin / : / Ferric enterobactin receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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
DepositionApr 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 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 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)79,2814
Polymers78,7441
Non-polymers5363
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-11 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.640, 158.080, 78.990
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: 78744.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / 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-95B / Azotochelin


Mass: 418.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N2O8
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2

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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: 65.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: PEG 8000, ADA, Magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.78→86.64 Å / Num. obs: 28035 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.8
Reflection shellResolution: 2.78→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.057 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2036 / CC1/2: 0.677 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m9k

1m9k


Resolution: 2.78→86.64 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.922 / SU B: 34.384 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R: 0.655 / ESU R Free: 0.331 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26025 1364 4.9 %RANDOM
Rwork0.22381 ---
obs0.22558 26627 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 107.054 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2--2.28 Å20 Å2
3----5.09 Å2
Refinement stepCycle: 1 / Resolution: 2.78→86.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 35 0 5398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025515
X-RAY DIFFRACTIONr_bond_other_d0.0010.024866
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9537472
X-RAY DIFFRACTIONr_angle_other_deg0.6833.00111305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9365696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.68624.328268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2715879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.461540
X-RAY DIFFRACTIONr_chiral_restr0.0910.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021136
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_it5.9346.132790
X-RAY DIFFRACTIONr_mcbond_other5.936.1282789
X-RAY DIFFRACTIONr_mcangle_it7.8839.2173484
X-RAY DIFFRACTIONr_mcangle_other7.8849.2193485
X-RAY DIFFRACTIONr_scbond_it6.0886.4622725
X-RAY DIFFRACTIONr_scbond_other6.0886.4632726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3859.5563989
X-RAY DIFFRACTIONr_long_range_B_refined10.8322934
X-RAY DIFFRACTIONr_long_range_B_other10.8322934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 96 -
Rwork0.34 1936 -
obs--99.85 %
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)
12.2757-0.1628-0.45233.6383-0.77546.1690.0774-0.1084-0.07470.82710.1509-0.0013-0.4429-0.244-0.22830.2130.0399-0.02680.05630.06320.211-1.33127.0918-12.9656
22.3567-1.0048-0.95523.51491.51787.9131-0.085-0.09650.32780.5367-0.0599-0.4955-0.70310.88420.14490.3044-0.2297-0.10340.23150.09780.54589.28135.2357-15.3523
33.1-1.0298-1.57462.71380.21084.7260.1523-0.19360.52980.33640.0992-0.1461-1.54610.5483-0.25150.5945-0.15240.04550.13180.10750.44550.897841.0354-17.7395
43.3764-0.3981-1.93792.60470.04867.4780.018-0.10870.17260.5219-0.05080.3333-1.3619-0.19670.03280.46450.13020.04920.14940.1250.5305-9.357239.828-17.4704
515.84226.519213.799878.121516.058313.4589-0.7992-0.7985-0.4923-1.59031.08710.4071-0.8805-0.4312-0.28790.8161-0.17780.36441.09950.24010.5919-30.516.4538.0644
61.2946-0.91590.1613.7856-1.78445.46650.06140.163-0.19920.40520.52661.0256-0.068-1.4087-0.58790.11120.02170.02680.50670.2040.5405-16.837526.0457-21.0212
73.0452-0.6358-1.35994.6961-1.975912.66470.29220.4822-0.2527-0.7720.25810.70270.5555-0.7332-0.55030.2067-0.0083-0.19860.5950.06120.437-15.218829.4113-43.9262
81.0697-0.2405-1.0946.1266-3.79163.975-0.34080.1258-0.1908-0.50.22530.09231.0397-0.27880.11550.6319-0.0514-0.05590.0915-0.07680.28621.274111.7632-17.9266
92.5927-0.6260.46853.9288-1.58545.72160.20930.2895-0.0960.4052-0.4357-0.9180.2591.59790.22650.11240.094-0.10610.47430.10160.426313.667720.8691-18.2505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 166
2X-RAY DIFFRACTION2A167 - 242
3X-RAY DIFFRACTION3A243 - 296
4X-RAY DIFFRACTION4A297 - 355
5X-RAY DIFFRACTION5A356 - 360
6X-RAY DIFFRACTION6A361 - 529
7X-RAY DIFFRACTION7A530 - 561
8X-RAY DIFFRACTION8A562 - 646
9X-RAY DIFFRACTION9A647 - 721

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