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Yorodumi- PDB-5fok: Crystal structure of the siderophore receptor PiuA from Pseudomon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fok | ||||||
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Title | Crystal structure of the siderophore receptor PiuA from Pseudomonas aeruginosa | ||||||
Components | IRON TRANSPORT OUTER MEMBRANE RECEPTOR | ||||||
Keywords | METAL TRANSPORT / TONB-DEPENDENT RECEPTOR / 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 | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Moynie, L. / 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 | 5fok.cif.gz | 527.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fok.ent.gz | 437.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fok.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fok_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5fok_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5fok_validation.xml.gz | 51 KB | Display | |
Data in CIF | 5fok_validation.cif.gz | 73.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/5fok ftp://data.pdbj.org/pub/pdb/validation_reports/fo/5fok | HTTPS FTP |
-Related structure data
Related structure data | 5fp1C 5fp2C 5fr8C 2fcpS 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 27 - 720 / Label seq-ID: 28 - 721
NCS oper: (Code: given Matrix: (0.978, 0.0522, 0.202), Vector: |
-Components
#1: Protein | Mass: 80412.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: G3XCY8 #2: Chemical | ChemComp-C8E / ( #3: Chemical | #4: Chemical | #5: 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: 2.89 Å3/Da / Density % sol: 57.44 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 32% PEG 400, 0.05 M TRIS PH 8.5, 0.05 M SODIUM SULPHATE AND 0.05 M LICL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→71.93 Å / Num. obs: 142771 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FCP Resolution: 1.9→71.93 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.251 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 30.477 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→71.93 Å
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Refine LS restraints |
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