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- PDB-8iut: Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8iut | ||||||
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Title | Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase with reduced Cys86 | ||||||
![]() | N(omega)-hydroxy-L-arginine amidinohydrolase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() Nomega-hydroxy-L-arginine amidinohydrolase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / arginase activity / arginine catabolic process to ornithine / antibiotic biosynthetic process / manganese ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oda, K. / Matoba, Y. | ||||||
Funding support | 1items
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![]() | ![]() Title: Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd Authors: Oda, K. / Komaguchi, K. / Matoba, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.9 KB | Display | ![]() |
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PDB format | ![]() | 98.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8iusC ![]() 8iuuC ![]() 8iuvC ![]() 8iuwC 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: 30016.701 Da / Num. of mol.: 2 / Fragment: N(omega)-hydroxy-L-arginine amidinohydrolase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D2Z025, Nomega-hydroxy-L-arginine amidinohydrolase |
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-Non-polymers , 5 types, 555 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/CU1.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-CU / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: PEG 4000, MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.35 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→43.65 Å / Num. obs: 59923 / % possible obs: 93 % / Redundancy: 2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.061 / Rrim(I) all: 0.09 / Χ2: 0.73 / Net I/σ(I): 6.2 / Num. measured all: 122601 |
Reflection shell | Resolution: 1.58→1.61 Å / % possible obs: 86.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.475 / Num. measured all: 5828 / Num. unique obs: 2774 / CC1/2: 0.648 / Rpim(I) all: 0.439 / Rrim(I) all: 0.648 / Χ2: 0.85 / Net I/σ(I) obs: 1.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 1.58→43.65 Å
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Refine LS restraints |
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LS refinement shell |
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