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Yorodumi- PDB-6r5s: Structure of the SBP FpvC from pseudomonas aeruginosa in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r5s | ||||||
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Title | Structure of the SBP FpvC from pseudomonas aeruginosa in complex with Fe(II) | ||||||
Components | Adhesion protein | ||||||
Keywords | TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Morera, S. / Vigouroux, A. | ||||||
Citation | Journal: Febs J. / Year: 2020 Title: A unique ferrous iron binding mode is associated with large conformational changes for the transport protein FpvC of Pseudomonas aeruginosa. Authors: Vigouroux, A. / Aumont-Nicaise, M. / Boussac, A. / Marty, L. / Lo Bello, L. / Legrand, P. / Brillet, K. / Schalk, I.J. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r5s.cif.gz | 226.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r5s.ent.gz | 182.2 KB | Display | PDB format |
PDBx/mmJSON format | 6r5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/6r5s ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r5s | HTTPS FTP |
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-Related structure data
Related structure data | 6r3zSC 6r44C 6r6kC 6ru4C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 32527.348 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: psaA, C0044_17990, CAZ10_34375, DZ962_30765, NCTC13719_02701, PAMH19_5875 Production host: Escherichia coli (E. coli) / References: UniProt: A0A069PX18, UniProt: Q9I174*PLUS #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 44.15 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: PEG 6K, 0.1 M Mes |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.738 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.738 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→37.62 Å / Num. obs: 14604 / % possible obs: 96.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 71.61 Å2 / Rsym value: 0.01 / Net I/σ(I): 9.35 |
Reflection shell | Resolution: 2.75→2.91 Å / Num. unique obs: 4343 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R3Z Resolution: 2.75→37.62 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.353
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Displacement parameters | Biso mean: 57 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→37.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.77 Å / Total num. of bins used: 36
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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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