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Yorodumi- PDB-2w77: Structures of P. aeruginosa FpvA bound to heterologous pyoverdine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w77 | ||||||
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Title | Structures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(Pfl18.1)-Fe complex | ||||||
Components |
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Keywords | RECEPTOR / TONB BOX / TRANSPORT / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / TONB-DEPENDENT TRANSPORTER | ||||||
Function / homology | Function and homology information pyoverdine biosynthetic process / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) PSEUDOMONAS FLUORESCENS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Greenwald, J. / Nader, M. / Celia, H. / Gruffaz, C. / Meyer, J.-M. / Schalk, I.J. / Pattus, F. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2009 Title: Fpva Bound to Non-Cognate Pyoverdines: Molecular Basis of Siderophore Recognition by an Iron Transporter. Authors: Greenwald, J. / Nader, M. / Celia, H. / Gruffaz, C. / Geoffroy, V. / Meyer, J.M. / Schalk, I.J. / Pattus, F. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 22-STRANDED BARREL THIS IS REPRESENTED BY A 23-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w77.cif.gz | 316.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w77.ent.gz | 252.7 KB | Display | PDB format |
PDBx/mmJSON format | 2w77.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w77_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2w77_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2w77_validation.xml.gz | 56 KB | Display | |
Data in CIF | 2w77_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w77 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w77 | HTTPS FTP |
-Related structure data
Related structure data | 2w16C 2w6tC 2w6uC 2w75C 2w76C 2w78C 2o5pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
-Non-polymers , 4 types, 14 molecules
#3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-PVE / ( | 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 18-1 Fe Complex #6: Chemical | ChemComp-FE / | 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 18-1 Fe Complex |
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-Details
Compound details | PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINE |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.35 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→107 Å / Num. obs: 57387 / % possible obs: 96.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.2 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O5P Resolution: 2.9→25.57 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.86 / SU B: 28.665 / SU ML: 0.253 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.955 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 23.32 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→25.57 Å
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Refine LS restraints |
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