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Yorodumi- PDB-7r3p: Apoform of the periplasmic FtrA/P19 protein from Rubrivivax gelat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r3p | ||||||
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Title | Apoform of the periplasmic FtrA/P19 protein from Rubrivivax gelatinosus (His-tag) | ||||||
Components | FtrA-P19 protein | ||||||
Keywords | TRANSPORT PROTEIN / COPPER BINDING / IRON TRANSPORT | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Rubrivivax gelatinosus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å | ||||||
Authors | Morera, S. / Vigouroux, A. | ||||||
Funding support | France, 1items
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Citation | Journal: Febs J. / Year: 2022 Title: New insights into the mechanism of iron transport through the bacterial Ftr system present in pathogens. Authors: Steunou, A.S. / Vigouroux, A. / Aumont-Nicaise, M. / Plancqueel, S. / Boussac, A. / Ouchane, S. / Morera, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r3p.cif.gz | 147.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r3p.ent.gz | 114.6 KB | Display | PDB format |
PDBx/mmJSON format | 7r3p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/7r3p ftp://data.pdbj.org/pub/pdb/validation_reports/r3/7r3p | HTTPS FTP |
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-Related structure data
Related structure data | 7r3sC 7r4uC 7r4vC 7r4zC 7r5eC 7r5gC 7r5pC 3lzlS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19473.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rubrivivax gelatinosus (bacteria) / Gene: EV684_12117 / Production host: Escherichia coli BL21(DE3) (bacteria) #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.52 Å3/Da / Density % sol: 51.25 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 2 M AS, 0.1 M citrate sodium |
-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: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→48.12 Å / Num. obs: 78363 / % possible obs: 99.7 % / Redundancy: 13 % / Biso Wilson estimate: 21.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.4→1.48 Å / Num. unique obs: 12299 / CC1/2: 0.718 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LZL Resolution: 1.4→48.12 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.057 / SU Rfree Blow DPI: 0.058 / SU Rfree Cruickshank DPI: 0.054
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Displacement parameters | Biso max: 112.96 Å2 / Biso mean: 26.52 Å2 / Biso min: 13.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→48.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.41 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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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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