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Open data
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Basic information
Entry | Database: PDB / ID: 7r3s | ||||||
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Title | FtrA/P19 of Rubrivivax gelatinosus in complex with Ni | ||||||
![]() | FtrA-P19 protein | ||||||
![]() | TRANSPORT PROTEIN / COPPER BINDING / IRON TRANSPORT | ||||||
Function / homology | NICKEL (II) ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Morera, S. / Vigouroux, A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.8 KB | Display | ![]() |
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PDB format | ![]() | 113.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448 KB | Display | ![]() |
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Full document | ![]() | 449.5 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r3pSC ![]() 7r4uC ![]() 7r4vC ![]() 7r4zC ![]() 7r5eC ![]() 7r5gC ![]() 7r5pC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19473.951 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 232 molecules ![](data/chem/img/NI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NI / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 2M AS, 0.1 M Citrate Sodium, 0.02 M NiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.48484 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→47.59 Å / Num. obs: 68702 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 35.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.79→1.9 Å / Num. unique obs: 10524 / CC1/2: 0.561 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7R3P Resolution: 1.79→47.59 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.1
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Displacement parameters | Biso max: 122.73 Å2 / Biso mean: 39.3 Å2 / Biso min: 21.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.79→47.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.81 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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