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Yorodumi- PDB-2w78: Structures of P. aeruginosa FpvA bound to heterologous pyoverdine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w78 | ||||||
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Title | Structures of P. aeruginosa FpvA bound to heterologous pyoverdines: FpvA-Pvd(ATCC13535)-Fe complex | ||||||
Components |
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Keywords | RECEPTOR / FPVA / IRON / MEMBRANE / 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: 3 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 | 2w78.cif.gz | 315.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w78.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 2w78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/2w78 ftp://data.pdbj.org/pub/pdb/validation_reports/w7/2w78 | HTTPS FTP |
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-Related structure data
Related structure data | 2w16C 2w6tC 2w6uC 2w75C 2w76C 2w77C 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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1 |
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2 |
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Unit cell |
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-Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 86556.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PPVR2 / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / Strain (production host): K691 / References: UniProt: P48632 #2: Protein/peptide | | Mass: 823.892 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PPVR2 / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / Strain (production host): K691 |
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-Non-polymers , 4 types, 14 molecules
#3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-PVE / ( | #6: Chemical | ChemComp-FE / | |
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-Details
Sequence details | SIGNAL PEPTIDE (RESIDUES 1-43) IS NOT IN THE CRYSTALLIZ |
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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: 3.86 Å3/Da / Density % sol: 67.88 % / Description: NONE |
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Crystal grow | Details: 1.3M NAH2PO4, 0.1M MES, PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.817 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.817 Å / Relative weight: 1 |
Reflection | Resolution: 3→107 Å / Num. obs: 50836 / % possible obs: 96.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.7 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2O5P Resolution: 3→97.59 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 30.657 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / 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: 45.48 Å2
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Refinement step | Cycle: LAST / Resolution: 3→97.59 Å
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