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Yorodumi- PDB-5fp1: Crystal structure of the siderophore receptor PiuA from Acinetoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fp1 | ||||||
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Title | Crystal structure of the siderophore receptor PiuA from Acinetobacter baumannii | ||||||
Components | TONB-DEPENDENT SIDEROPHORE RECEPTOR | ||||||
Keywords | METAL TRANSPORT / SIDEROPHORE RECEPTOR / OUTER-MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | ACINETOBACTER BAUMANNII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | ||||||
Authors | Moynie, L. / Tortajada, A. / Naismith, J.H. | ||||||
Citation | Journal: Antimicrob. Agents Chemother. / Year: 2017 Title: Structure and Function of the PiuA and PirA Siderophore-Drug Receptors from Pseudomonas aeruginosa and Acinetobacter baumannii. Authors: Moynie, L. / Luscher, A. / Rolo, D. / Pletzer, D. / Tortajada, A. / Weingart, H. / Braun, Y. / Page, M.G. / Naismith, J.H. / Kohler, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fp1.cif.gz | 168.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fp1.ent.gz | 132.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fp1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fp1 ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fp1 | HTTPS FTP |
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-Related structure data
Related structure data | 5fokSC 5fp2C 5fr8C 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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Unit cell |
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-Components
#1: Protein | Mass: 78665.672 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-743 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Plasmid: PTAMAHISTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: D0CAH3 | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-C8E / ( #4: Water | ChemComp-HOH / | |
-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: 45 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 1 M DIAMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91741 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→65.29 Å / Num. obs: 104869 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.94→1.99 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FOK Resolution: 1.94→65.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.854 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.297 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→65.29 Å
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Refine LS restraints |
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