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Yorodumi- PDB-8iuv: Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iuv | ||||||
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Title | Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86 | ||||||
Components | N(omega)-hydroxy-L-arginine amidinohydrolase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 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 | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Oda, K. / Matoba, Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8iuv.cif.gz | 126 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iuv.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 8iuv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8iuv_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8iuv_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8iuv_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 8iuv_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/8iuv ftp://data.pdbj.org/pub/pdb/validation_reports/iu/8iuv | HTTPS FTP |
-Related structure data
Related structure data | 8iusC 8iuuC 8iuwC 9iq9C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptomyces lavendulae (bacteria) / Gene: dcsB / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: D2Z025, Nomega-hydroxy-L-arginine amidinohydrolase #2: Chemical | ChemComp-MN / | #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.96 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
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: 1.75→43.92 Å / Num. obs: 44308 / % possible obs: 96.8 % / Redundancy: 3.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.048 / Rrim(I) all: 0.092 / Χ2: 0.91 / Net I/σ(I): 9.8 / Num. measured all: 158923 |
Reflection shell | Resolution: 1.75→1.78 Å / % possible obs: 95.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.351 / Num. measured all: 8413 / Num. unique obs: 2372 / CC1/2: 0.884 / Rpim(I) all: 0.217 / Rrim(I) all: 0.413 / Χ2: 0.57 / Net I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.92 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 18.98 / 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: 1.75→43.92 Å
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Refine LS restraints |
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LS refinement shell |
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