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- PDB-5nec: Crystal structure of the siderophore receptor PiuD from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 5nec
TitleCrystal structure of the siderophore receptor PiuD from Pseudomonas aeruginosa
ComponentsTonB-dependent siderophore receptor
KeywordsMEMBRANE PROTEIN / PiuD / outer membrane receptor
Function / homology
Function and homology information


: / siderophore uptake transmembrane transporter activity / membrane => GO:0016020 / cell outer membrane / signaling receptor activity
Similarity search - Function
Catecholate siderophore receptor Fiu / TonB-dependent receptor-like / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / 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, plug domain superfamily ...Catecholate siderophore receptor Fiu / TonB-dependent receptor-like / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / 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, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent Receptor Plug Domain / TonB-dependent receptor-like, beta-barrel domain superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Putative outer membrane receptor for iron transport
Similarity search - Component
Biological speciesPseudomonas aeruginosa 39016 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMoynie, L. / Naismith, J.H.
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: TonB-Dependent Receptor Repertoire of Pseudomonas aeruginosa for Uptake of Siderophore-Drug Conjugates.
Authors: Luscher, A. / Moynie, L. / Auguste, P.S. / Bumann, D. / Mazza, L. / Pletzer, D. / Naismith, J.H. / Kohler, T.
History
DepositionMar 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TonB-dependent siderophore receptor
B: TonB-dependent siderophore receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,6234
Polymers163,0102
Non-polymers6132
Water1,17165
1
A: TonB-dependent siderophore receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1183
Polymers81,5051
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TonB-dependent siderophore receptor


Theoretical massNumber of molelcules
Total (without water)81,5051
Polymers81,5051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.522, 136.452, 118.955
Angle α, β, γ (deg.)90.00, 132.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 27 - 732 / Label seq-ID: 29 - 734

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein TonB-dependent siderophore receptor


Mass: 81504.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa 39016 (bacteria)
Gene: PAMH27_5021 / Production host: Escherichia coli (E. coli) / References: UniProt: V6ALN4
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.09 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 9 / Details: PEG MME 5000, Bicine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. obs: 86146 / % possible obs: 97.6 % / Redundancy: 3.58 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 9.86
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.94 % / Rmerge(I) obs: 1.044 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 7235 / CC1/2: 0.569 / % possible all: 85.1

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Processing

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

5fok


Resolution: 2.3→91.03 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 20.192 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.208 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24911 4250 5 %RANDOM
Rwork0.22253 ---
obs0.2239 80547 98.44 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 56.361 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å2-0.03 Å2
2---2.67 Å20 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.3→91.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10073 0 16 65 10154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210325
X-RAY DIFFRACTIONr_bond_other_d0.0020.029319
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9314020
X-RAY DIFFRACTIONr_angle_other_deg0.884321403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61251269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5324.242521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.261151592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1451564
X-RAY DIFFRACTIONr_chiral_restr0.0850.21507
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022553
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_it1.7494.655118
X-RAY DIFFRACTIONr_mcbond_other1.7494.655117
X-RAY DIFFRACTIONr_mcangle_it2.9026.9586373
X-RAY DIFFRACTIONr_mcangle_other2.9026.9586374
X-RAY DIFFRACTIONr_scbond_it2.14.9895206
X-RAY DIFFRACTIONr_scbond_other2.14.9895207
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4947.3677647
X-RAY DIFFRACTIONr_long_range_B_refined5.26451.88510479
X-RAY DIFFRACTIONr_long_range_B_other5.26351.8810471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 40694 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.303→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 274 -
Rwork0.353 5236 -
obs--86.69 %
Refinement TLS params.

S23: -0.0533 Å ° / 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 °)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)
10.40530.30450.16910.40230.19050.2879-0.03520.05870.0759-0.0610.0278-0.11910.08340.00730.0815-0.01010.00330.04870.02210.086929.321921.8136-21.7638
20.3336-0.1755-0.10120.32260.29360.4083-0.0347-0.07990.09910.08140.0496-0.04020.0339-0.0150.12970.0045-0.02720.0207-0.02090.035221.624122.151828.878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 732
2X-RAY DIFFRACTION2B27 - 732

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