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Yorodumi- PDB-5fr8: Crystal structure of the siderophore receptor PirA from Acinetoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fr8 | ||||||
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Title | Crystal structure of the siderophore receptor PirA from Acinetobacter baumannii | ||||||
Components | TONB-DEPENDENT SIDEROPHORE RECEPTOR | ||||||
Keywords | TRANSPORT PROTEIN / TONB-DEPENDENT RECEPTOR / OUTER-MEMBRANE PROTEIN | ||||||
Function / homology | Function and homology information : / siderophore uptake transmembrane transporter activity / cell outer membrane / signaling receptor activity Similarity search - Function | ||||||
Biological species | ACINETOBACTER BAUMANNII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" 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 "BC" 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 | 5fr8.cif.gz | 558.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fr8.ent.gz | 465.2 KB | Display | PDB format |
PDBx/mmJSON format | 5fr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5fr8 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5fr8 | HTTPS FTP |
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-Related structure data
Related structure data | 5fokC 5fp1C 5fp2C 1fepS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 24 - 730 / Label seq-ID: 27 - 733
NCS oper: (Code: given Matrix: (-0.4995, -0.8662, 0.0147), Vector: |
-Components
#1: Protein | Mass: 80593.797 Da / Num. of mol.: 2 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: D0C8V9 #2: Chemical | #3: 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: 4.44 Å3/Da / Density % sol: 72 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 16% PEG 8000, 0.15 M MAGNESIUM SULFATE BICINE PH 9 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 | |||||||||||||||
Detector | Type: DECTRIS PIXEL / Detector: PIXEL / Date: Aug 6, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.83→85.81 Å / Num. obs: 62752 / % possible obs: 90.7 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5 | |||||||||||||||
Reflection shell | Resolution: 2.83→2.98 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.4 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FEP Resolution: 2.83→84.6 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.891 / SU B: 24.586 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.07 / 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: 69.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2.83→84.6 Å
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Refine LS restraints |
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