[English] 日本語
Yorodumi- PDB-1xkh: Pyoverdine outer membrane receptor FpvA from Pseudomonas aerugino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xkh | ||||||
---|---|---|---|---|---|---|---|
Title | Pyoverdine outer membrane receptor FpvA from Pseudomonas aeruginosa PAO1 bound to pyoverdine | ||||||
Components |
| ||||||
Keywords | MEMBRANE PROTEIN / PYOVERDINE / FPVA / TONB BOX / SIDEROPHORE / CELL MEMBRANE / ION TRANSPORT / TONB DEPENDENT RECEPTOR | ||||||
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: 3.6 Å | ||||||
Authors | Cobessi, D. / Celia, H. / Folschweiller, N. / Schalk, I.J. / Abdallah, M.A. / Pattus, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The Crystal Structure of the Pyoverdine Outer Membrane Receptor FpvA from Pseudomonas aeruginosa at 3.6A Resolution Authors: Cobessi, D. / Celia, H. / Folschweiller, N. / Schalk, I.J. / Abdallah, M.A. / Pattus, F. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Crystallization and preliminary X-ray analysis of the outer membrane pyoverdine receptor FpvA from Pseudomonas aeruginosa Authors: Cobessi, D. / Celia, H. / Folschweiller, N. / Heymann, M. / Schalk, I.J. / Abdallah, M.A. / Pattus, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xkh.cif.gz | 420.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xkh.ent.gz | 343.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xkh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/1xkh ftp://data.pdbj.org/pub/pdb/validation_reports/xk/1xkh | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 78015.758 Da / Num. of mol.: 3 / Fragment: residues 129-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fpva / Plasmid: PVR2 / Production host: Pseudomonas aeruginosa (bacteria) / Strain (production host): PAO503 / References: UniProt: P48632 #2: Protein/peptide | Type: PolypeptidePeptide / Class: Metal transport / Mass: 997.062 Da / Num. of mol.: 3 / 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 CHROMOPHORE #3: Chemical | #4: Chemical | Type: PolypeptidePeptide / Class: Metal transport / Mass: 376.341 Da / Num. of mol.: 3 / 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 CHROMOPHORE Compound details | PYOVERDINES ARE A GROUP OF STRUCTURALLY RELATED SIDEROPHORES PRODUCED BY FLUORESCENT PSEUDOMONAS ...PYOVERDINE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.8 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 13-16% PEG 4000, 20-25% ethylene glycol as cryoprectant in a 0.1M sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979413, 0.979632, 0.977801 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 3, 2003 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 3.6→20 Å / Num. all: 41896 / Num. obs: 41896 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Rsym value: 0.129 / Net I/σ(I): 8.46 | ||||||||||||
Reflection shell | Resolution: 3.6→3.7 Å / Mean I/σ(I) obs: 1.14 / Rsym value: 0.375 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Ferrichrome outer membrane receptor FhuA from Escherichia coli. Resolution: 3.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 3.6→3.73 Å
|