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- PDB-5on5: Crystal structure of NikA in complex with Fe-L2 (Fe-L2 (N-(2-hydr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5on5 | ||||||
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Title | Crystal structure of NikA in complex with Fe-L2 (Fe-L2 (N-(2-hydroxy-3-methoxybenzyl)-N'-(2-thiomethylbenzyl)- N,N'-ethylenediamine diacetic acid) after dioxygen oxidation | ||||||
![]() | Nickel-binding periplasmic protein | ||||||
![]() | METAL BINDING PROTEIN / artificial oxygenase / CLEC / dioxygen activation / oxidation of carbon-carbon double bonds | ||||||
Function / homology | ![]() nickel cation import across plasma membrane / metal cluster binding / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space ...nickel cation import across plasma membrane / metal cluster binding / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space / heme binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cavazza, C. / Menage, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cross-Linked Artificial Enzyme Crystals as Heterogeneous Catalysts for Oxidation Reactions. Authors: Lopez, S. / Rondot, L. / Lepretre, C. / Marchi-Delapierre, C. / Menage, S. / Cavazza, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.7 KB | Display | ![]() |
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PDB format | ![]() | 187.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 47.8 KB | Display | |
Data in CIF | ![]() | 71.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5on0C ![]() 5on1C ![]() 5on4C ![]() 5on8C ![]() 5on9C ![]() 3mvwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 56360.734 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: nikA, b3476, JW3441 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 1007 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/9YH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/9YH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 mM sodium acetate, pH 4.6 1.7 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.13 Å / Num. obs: 112813 / % possible obs: 99.9 % / Redundancy: 6.81 % / Net I/σ(I): 18.82 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MVW Resolution: 1.7→43.41 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→43.41 Å
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Refine LS restraints |
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LS refinement shell |
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