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- PDB-7eun: Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7eun | ||||||
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Title | Crystal structure of N(omega)-hydroxy-L-arginine hydrolase in complex with ABH | ||||||
![]() | N(omega)-hydroxy-L-arginine amidinohydrolase | ||||||
![]() | ANTIBIOTIC / 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: Catalytic mechanism of DcsB: Arginase framework used for hydrolyzing its inhibitor. Authors: Oda, K. / Sakaguchi, T. / 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 | ![]() | 330.8 KB | Display | ![]() |
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PDB format | ![]() | 273.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5 MB | Display | ![]() |
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Full document | ![]() | 5 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 41.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7eukC ![]() 7eulC ![]() 7euqC ![]() 6luhS 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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2 | ![]()
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Unit cell |
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Components
#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 #2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-ABH / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % / Mosaicity: 0.1 ° |
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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: Feb 14, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.28→44.26 Å / Num. obs: 116740 / % possible obs: 95.5 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Net I/σ(I): 10.9 / Num. measured all: 428211 / Scaling rejects: 239 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdbid 6LUH Resolution: 1.28→44.26 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 12.41 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.07 Å2 / Biso mean: 16.5292 Å2 / Biso min: 5.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→44.26 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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