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- PDB-5jqn: NitN Amidase from Neterenkonia sp. AN1 after thrombin His-tag removal. -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jqn | ||||||
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Title | NitN Amidase from Neterenkonia sp. AN1 after thrombin His-tag removal. | ||||||
![]() | Aliphatic amidase | ||||||
![]() | HYDROLASE / NitN Amidase / Neterenkonia sp. AN1 | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sewell, B.T. / Kimani, S.W. / Weber, B.W. | ||||||
![]() | ![]() Title: QM/MM Modelling of Substrate Binding in the Amidase Active Site Authors: Sewell, B.T. / Kimani, S.W. / Venter, G.A. / Hunter, R. / Schell, D.T. #1: ![]() Title: Unique aliphatic amidase from a psychrotrophic and haloalkaliphilic nesterenkonia isolate. Authors: Nel, A.J. / Tuffin, I.M. / Sewell, B.T. / Cowan, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.9 KB | Display | ![]() |
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PDB format | ![]() | 48.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.1 KB | Display | ![]() |
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Full document | ![]() | 424.5 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3hkxS S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28243.664 Da / Num. of mol.: 1 / Mutation: GSH arising from the N-terminal His-tag. Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2M Ammonium Sufate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 8, 2015 / Details: Toroidal Mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→45.566 Å / Num. obs: 91215 / % possible obs: 98.6 % / Redundancy: 5.6 % / Rrim(I) all: 0.037 / Net I/σ(I): 25.13 / Num. measured all: 580951 |
Reflection shell | Highest resolution: 1.19 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3HKX Resolution: 1.19→45.566 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.19→45.566 Å
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Refine LS restraints |
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LS refinement shell |
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