+Open data
-Basic information
Entry | Database: PDB / ID: 2w16 | ||||||
---|---|---|---|---|---|---|---|
Title | Structures of FpvA bound to heterologous pyoverdines | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / FPVA / IRON / MEMBRANE / RECEPTOR / TONB BOX / TRANSPORT / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / IRON TRANSPORT / CELL OUTER MEMBRANE / 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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 |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE", "BE" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE", "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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2w16.cif.gz | 314.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2w16.ent.gz | 252.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w16.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w16_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2w16_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2w16_validation.xml.gz | 54.7 KB | Display | |
Data in CIF | 2w16_validation.cif.gz | 74.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/2w16 ftp://data.pdbj.org/pub/pdb/validation_reports/w1/2w16 | HTTPS FTP |
-Related structure data
Related structure data | 2w6tC 2w6uC 2w75C 2w76C 2w77C 2w78C 2o5pS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 C-E 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 C-E Fe Complex |
---|
-Details
Compound details | PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINE |
---|---|
Nonpolymer details | (1S)-5-AMINO-2,3-DIHYDRO-8,9-DIHYDROXY-1H-PYRIMIDO[1, 2A]CHINOLIN-1-CARBOXYLIC ACID (PVE): PVE IS ...(1S)-5-AMINO-2,3-DIHYDRO-8,9-DIHYDROXY-1H-PYRIMIDO[1, 2A]CHINOLIN-1-CARBOXYLIC |
Sequence details | SIGNAL PEPTIDE (RESIDUES 1-43) IS NOT IN THE CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.96 Å3/Da / Density % sol: 68.67 % / Description: NONE |
---|---|
Crystal grow | Details: 1.3M NAH2PO4, 0.1M MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8423 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→100 Å / Num. obs: 70306 / % possible obs: 95.4 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.7 / % possible all: 95.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O5P Resolution: 2.71→107.83 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / SU B: 22.799 / SU ML: 0.215 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.527 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.67 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→107.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|