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- PDB-2iah: Crystal structure of the ferripyoverdine receptor of the outer me... -

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Basic information

Entry
Database: PDB / ID: 2iah
TitleCrystal structure of the ferripyoverdine receptor of the outer membrane of Pseudomonas aeruginosa bound to ferripyoverdine.
Components
  • Ferripyoverdine receptor
  • Pyoverdin C-E
KeywordsMEMBRANE PROTEIN / PYOVERDINE / FPVA / TONB BOX / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / TONB DEPENDENT RECEPTOR
Function / homology
Function and homology information


pyoverdine biosynthetic process / siderophore-iron import into cell / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane
Similarity search - Function
Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / TonB-dependent receptor, beta-barrel domain / TonB-dependent siderophore receptor / TonB-dependent receptor, conserved site ...Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Secretin and TonB N terminus short domain / Secretin/TonB, short N-terminal domain / Secretin and TonB N terminus short domain / TonB-dependent receptor, plug domain / Ferric Hydroxamate Uptake Protein; Chain A, domain 1 / 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 / 3-Layer(bab) Sandwich / Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PYOVERDIN C-E Fe Complex / : / Chem-PVE / : / Ferripyoverdine receptor
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsWirth, C. / Pattus, F. / Cobessi, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: From the periplasmic signaling domain to the extracellular face of an outer membrane signal transducer of Pseudomonas aeruginosa: crystal structure of the ferric pyoverdine outer membrane receptor.
Authors: Wirth, C. / Meyer-Klaucke, W. / Pattus, F. / Cobessi, D.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 27, 2011Group: Structure summary
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 6, 2013Group: Other
Revision 1.5May 13, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Aug 30, 2023Group: 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _struct_conn.ptnr2_label_seq_id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferripyoverdine receptor
I: Pyoverdin C-E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0815
Polymers87,5532
Non-polymers5283
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.123, 82.123, 286.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ferripyoverdine receptor


Mass: 86556.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fpva / Plasmid: pPVR2 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P48632
#2: Protein/peptide Pyoverdin C-E


Type: Polypeptide / Class: Metal transport / Mass: 997.062 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
Source: (synth.) Pseudomonas aeruginosa (bacteria) / References: NOR: NOR00190, PYOVERDIN C-E Fe Complex
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PVE / (1S)-1-CARBOXY-5-[(3-CARBOXYPROPANOYL)AMINO]-8,9-DIHYDROXY-1,2,3,4-TETRAHYDROPYRIMIDO[1,2-A]QUINOLIN-11-IUM


Type: Polypeptide / Class: Metal transport / Mass: 376.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18N3O7
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
References: PYOVERDIN C-E Fe Complex
#5: Chemical ChemComp-FE / FE (III) ION


Type: Polypeptide / Class: Metal transport / Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS ...Details: IN IRON-DEFICIENT CONDITIONS, PSEUDOMONAS AERUGINOSA SECRETES A MAJOR FLUORESCENT SIDEROPHORE NAMED PYOVERDIN (PVD), WHICH AFTER CHELATING IRON(III) IS TRANSPORTED BACK INTO THE CELL VIA ITS OUTER MEMBRANE RECEPTOR FPVA. FPVA IS A TONB-DEPENDENT TRANSPORT PROTEIN AND HAS THE ABILITY TO BIND PVD IN ITS APO- OR IRON-LOADED FORM.
References: PYOVERDIN C-E Fe Complex
Compound detailsPYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS SPECIES. PYOVERDINE IS NECESSARY FOR INFECTION IN SEVERAL DIFFERENT DISEASE MODELS. THE OCCURRENCE OF PYOVERDINE-DEFECTIVE STRAINS IN CHRONIC INFECTIONS OF PATIENTS WITH CYSTIC FIBROSIS AND THE EXTREMELY HIGH SEQUENCE DIVERSITY OF GENES INVOLVED IN PYOVERDINE SYNTHESIS AND UPTAKE INDICATE THAT PYOVERDINE PRODUCTION IS SUBJECT TO HIGH EVOLUTIONARY PRESSURE. PYOVERDINE-DEPENDENT IRON TRANSPORT IS ALSO CRUCIAL FOR BIOFILM DEVELOPMENT, FURTHER EXPANDING THE IMPORTANCE OF THESE SIDEROPHORES IN PSEUDOMONAS BIOLOGY. HERE, PYOVERDINE-CHROMOPHORE IRON(III) COMPLEX IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE OF CHAIN I (SEQRES) AND THE TWO LIGANDS (HET) PVE1I AND FE10I.

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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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Na Acetate 0.1 M, pH 4.6; 12 mM MgSO4, 12 % PEG 3350. Protein concentration in 0.5 % C8E4: 15 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.73→46.96 Å / Num. obs: 24636 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.045 / Net I/σ(I): 7.3
Reflection shellResolution: 2.73→2.88 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 2982 / Rsym value: 0.274 / % possible all: 78.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XKH

1xkh


Resolution: 2.73→46.96 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.879 / SU B: 40.321 / SU ML: 0.369 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28522 1193 4.8 %RANDOM
Rwork0.24412 ---
obs0.24611 23442 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.148 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.21 Å2
Refinement stepCycle: LAST / Resolution: 2.73→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5973 0 32 0 6005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226156
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.958374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54124.172302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67515930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3591536
X-RAY DIFFRACTIONr_chiral_restr0.0660.2879
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024854
X-RAY DIFFRACTIONr_nbd_refined0.1860.22170
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24068
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2153
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.220
X-RAY DIFFRACTIONr_mcbond_it0.2081.53816
X-RAY DIFFRACTIONr_mcangle_it0.29625962
X-RAY DIFFRACTIONr_scbond_it0.4932732
X-RAY DIFFRACTIONr_scangle_it0.6774.52412
LS refinement shellResolution: 2.73→2.803 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 63 -
Rwork0.332 1119 -
obs--100 %
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)
12.8687-0.76664.72726.35343.574511.83780.2035-0.0695-0.07790.3675-0.00830.12110.4579-0.6413-0.19520.28050.21470.00250.28530.08220.3976-22.074443.6955173.38
20.98470.1104-1.36180.368-0.5033.1059-0.0493-0.12130.06340.05040.07870.06740.22490.1921-0.0295-0.10090.1988-0.0547-0.116-0.0238-0.0703-7.310234.3585137.3335
30.8906-0.2848-0.3070.9095-0.16782.422-0.11460.0170.0649-0.11070.00060.04620.20930.13920.1139-0.18180.1288-0.0406-0.22320.0089-0.2014-6.712833.8736129.2749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA44 - 1181 - 75
2X-RAY DIFFRACTION2AA139 - 27696 - 233
3X-RAY DIFFRACTION3AA277 - 815234 - 772

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