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- PDB-5mzs: Crystal structure of the ferric enterobactin receptor (PfeA) muta... -

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Basic information

Entry
Database: PDB / ID: 5mzs
TitleCrystal structure of the ferric enterobactin receptor (PfeA) mutant (R480A_Q482A) from Pseudomonas aeruginosa
ComponentsFerric enterobactin receptor
KeywordsMEMBRANE PROTEIN / PfeA / PA2688 / outer membrane receptor
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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
DepositionFeb 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 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 / 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 1.3Oct 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


Theoretical massNumber of molelcules
Total (without water)78,6011
Polymers78,6011
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 area28700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.230, 156.860, 76.580
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: 78601.281 Da / Num. of mol.: 1 / Mutation: R480A_Q482A
Source method: isolated from a genetically manipulated source
Details: Mutants R480A Q482A
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / 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: 3.45 Å3/Da / Density % sol: 64.32 %
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: I24 / Wavelength: 0.96858 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.67→76.58 Å / Num. obs: 31598 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.5
Reflection shellResolution: 2.67→2.72 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.197 / Mean I/σ(I) obs: 1.4 / Num. unique all: 1564 / Num. unique obs: 9471 / CC1/2: 0.662 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m9b

5m9b


Resolution: 2.67→76.58 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 31.189 / SU ML: 0.274 / Cross valid method: THROUGHOUT / ESU R: 0.478 / ESU R Free: 0.307 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26597 1546 4.9 %RANDOM
Rwork0.21787 ---
obs0.22021 30008 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 85.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---2.47 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.67→76.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 0 7 5425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195530
X-RAY DIFFRACTIONr_bond_other_d0.0010.025071
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9477506
X-RAY DIFFRACTIONr_angle_other_deg0.771311651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.125705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.98724.424269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.17115884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3121539
X-RAY DIFFRACTIONr_chiral_restr0.1030.2804
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021315
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_it2.8354.1922823
X-RAY DIFFRACTIONr_mcbond_other2.8344.1922822
X-RAY DIFFRACTIONr_mcangle_it4.0976.2983527
X-RAY DIFFRACTIONr_mcangle_other4.0976.2973528
X-RAY DIFFRACTIONr_scbond_it2.9094.4572707
X-RAY DIFFRACTIONr_scbond_other2.9084.4562707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4066.5873979
X-RAY DIFFRACTIONr_long_range_B_refined6.34788.6811776
X-RAY DIFFRACTIONr_long_range_B_other6.34788.67611777
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 124 -
Rwork0.36 2206 -
obs--99.83 %
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)
12.344-0.026-0.2873.90950.3332.5049-0.02140.1872-0.1045-0.3499-0.02030.0821-0.03380.05670.04160.05420.0123-0.0150.08770.03230.2516-4.180326.5228-12.3436
22.28170.04760.15253.27051.05533.2288-0.06920.26280.1755-0.52040.0894-0.6358-0.53130.5288-0.02020.1766-0.13610.05880.17630.05040.504410.743234.6448-14.2102
34.8325-1.0433-2.53983.32652.83824.3810.1310.01240.4971-0.77810.0351-0.1019-1.20640.4443-0.16610.4412-0.1788-0.00510.16340.13140.4372-0.930841.3892-14.3809
41.758-0.3869-0.25862.18630.80333.2564-0.10180.40760.1349-0.3852-0.12270.2481-0.6201-0.17850.22450.28320.1065-0.09070.19560.03390.4165-12.92838.0745-16.1056
51.8761-0.5239-0.43943.041-0.2822.3772-0.07360.5319-0.0809-0.6133-0.06310.7291-0.0635-0.43490.13670.2789-0.0357-0.26830.2793-0.08120.4854-17.512123.8314-20.1011
60.7098-1.5375-0.41393.39380.88610.24760.45580.3297-0.1092-1.1251-0.4740.2379-0.2175-0.25260.01821.0185-0.2659-0.51921.25830.04350.535-16.138226.4296-40.3871
75.7258-1.00592.42426.3927-1.5135.8795-0.06620.6444-0.059-0.4918-0.10470.14930.4875-0.02530.17090.1995-0.0090.08510.1196-0.0940.4267-0.98869.5121-14.7872
84.0075-0.1223.96533.0051-2.169811.4127-0.10560.4774-0.1942-0.6096-0.0146-0.13830.1503-0.02720.12020.24010.08360.11340.2091-0.10520.44216.811613.6315-20.8866
92.373-0.8923-0.60545.84340.25860.2841-0.08770.2843-0.0318-0.2866-0.0534-1.36090.12950.08810.14110.14520.07560.20070.31680.07380.621614.18723.1852-14.6374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 154
2X-RAY DIFFRACTION2A155 - 238
3X-RAY DIFFRACTION3A239 - 298
4X-RAY DIFFRACTION4A299 - 382
5X-RAY DIFFRACTION5A383 - 529
6X-RAY DIFFRACTION6A530 - 567
7X-RAY DIFFRACTION7A568 - 613
8X-RAY DIFFRACTION8A614 - 661
9X-RAY DIFFRACTION9A662 - 721

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