+
Open data
-
Basic information
Entry | Database: PDB / ID: 5k8o | ||||||
---|---|---|---|---|---|---|---|
Title | Mn2+/5NSA-bound 5-nitroanthranilate aminohydrolase | ||||||
![]() | 5-nitroanthranilic acid aminohydrolase | ||||||
![]() | HYDROLASE / Nitroaromatics / deaminase / metalloenzyme | ||||||
Function / homology | ![]() 5-nitroanthranilic acid aminohydrolase / hydrolase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kalyoncu, S. | ||||||
![]() | ![]() Title: Enzymatic hydrolysis by transition-metal-dependent nucleophilic aromatic substitution. Authors: Kalyoncu, S. / Heaner, D.P. / Kurt, Z. / Bethel, C.M. / Ukachukwu, C.U. / Chakravarthy, S. / Spain, J.C. / Lieberman, R.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 626.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 522.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 502.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 529 KB | Display | |
Data in XML | ![]() | 108.6 KB | Display | |
Data in CIF | ![]() | 148.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k8mSC ![]() 5k8nC ![]() 5k8pC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 46400.555 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D3WZ85, 5-nitroanthranilic acid aminohydrolase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-6R7 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.52 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium cacodylate pH 6.5, 0.75 M trisodium citrate, 16 mM manganese chloride, 0.16 mM 5-nitrosalicylic acid Temp details: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→49.83 Å / Num. obs: 119036 / % possible obs: 92.23 % / Redundancy: 5.2 % / Net I/σ(I): 11.63 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5K8M Resolution: 2.893→49.828 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.61
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.893→49.828 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|