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Yorodumi- PDB-8iuw: Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8iuw | ||||||
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Title | Crystal structure of Copper-bound 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 / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 8iuw.cif.gz | 131.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8iuw.ent.gz | 100.8 KB | Display | PDB format |
PDBx/mmJSON format | 8iuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iu/8iuw ftp://data.pdbj.org/pub/pdb/validation_reports/iu/8iuw | HTTPS FTP |
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-Related structure data
Related structure data | 8iusC 8iutC 8iuuC 8iuvC 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
-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.) Streptomyces lavendulae (bacteria) / Gene: dcsB / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: D2Z025, Nomega-hydroxy-L-arginine amidinohydrolase |
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-Non-polymers , 5 types, 508 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CU / | #5: Chemical | ChemComp-CU1 / | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.02 Å3/Da / Density % sol: 39.15 % |
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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: 1.35 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: 1.35 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.22 Å / Num. obs: 70228 / % possible obs: 93.3 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Χ2: 1.04 / Net I/σ(I): 13.7 / Num. measured all: 256067 |
Reflection shell | Resolution: 1.5→1.53 Å / % possible obs: 87 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.704 / Num. measured all: 11971 / Num. unique obs: 3255 / CC1/2: 0.708 / Rpim(I) all: 0.426 / Rrim(I) all: 0.824 / Χ2: 0.75 / Net I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.22 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.65 / 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: 1.5→44.22 Å
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Refine LS restraints |
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LS refinement shell |
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