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- PDB-2iah: Crystal structure of the ferripyoverdine receptor of the outer me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iah | ||||||
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Title | Crystal structure of the ferripyoverdine receptor of the outer membrane of Pseudomonas aeruginosa bound to ferripyoverdine. | ||||||
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![]() | MEMBRANE PROTEIN / PYOVERDINE / FPVA / TONB BOX / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / TONB DEPENDENT RECEPTOR | ||||||
Function / homology | ![]() pyoverdine biosynthetic process / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wirth, C. / Pattus, F. / Cobessi, D. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.1 KB | Display | ![]() |
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PDB format | ![]() | 125.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 826.3 KB | Display | ![]() |
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Full document | ![]() | 834.4 KB | Display | |
Data in XML | ![]() | 27.4 KB | Display | |
Data in CIF | ![]() | 37.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xkhS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 86556.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | ![]() 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.) ![]() ![]() |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-PVE / (![]() 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 / ![]() 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 details | PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.86 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 5, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.148 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→46.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.73→2.803 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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