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Yorodumi- PDB-9iq9: Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hyd... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9iq9 | |||||||||
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Title | Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase with reduced Cys86 | |||||||||
Components | N(omega)-hydroxy-L-arginine amidinohydrolase | |||||||||
Keywords | HYDROLASE / N(omega)-hydroxy-L-arginine 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: 1.58 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 | 9iq9.cif.gz | 130.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9iq9.ent.gz | 99.9 KB | Display | PDB format |
PDBx/mmJSON format | 9iq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/9iq9 ftp://data.pdbj.org/pub/pdb/validation_reports/iq/9iq9 | HTTPS FTP |
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-Related structure data
Related structure data | 8iusC 8iuuC 8iuvC 8iuwC 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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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: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: D2Z025, Nomega-hydroxy-L-arginine amidinohydrolase #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | #5: 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: 2.02 Å3/Da / Density % sol: 39.16 % |
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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: 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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→43.65 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.53 / 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: 1.58→43.65 Å
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Refine LS restraints |
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LS refinement shell |
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