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Yorodumi- PDB-6luh: High resolution structure of N(omega)-hydroxy-L-arginine hydrolase -
+Open data
-Basic information
Entry | Database: PDB / ID: 6luh | ||||||
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Title | High resolution structure of N(omega)-hydroxy-L-arginine hydrolase | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | Oda, K. / Matoba, Y. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Crystal structure of an Nomega-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway. Authors: Oda, K. / Shimotani, N. / Kuroda, T. / Matoba, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6luh.cif.gz | 131.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6luh.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 6luh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6luh_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 6luh_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 6luh_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 6luh_validation.cif.gz | 42.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6luh ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6luh | HTTPS FTP |
-Related structure data
Related structure data | 6lugSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) 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: 2.01 Å3/Da / Density % sol: 38.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: PEG 4000, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.09 Å / Num. obs: 72157 / % possible obs: 96.5 % / Redundancy: 7.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Net I/σ(I): 11.2 / Num. measured all: 519387 / Scaling rejects: 2596 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.449 / Num. unique obs: 3541 / CC1/2: 0.9 / Rpim(I) all: 0.178 / Rrim(I) all: 0.484 / % possible all: 94.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6LUG Resolution: 1.5→44.09 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 23.97
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.32 Å2 / Biso mean: 14.1934 Å2 / Biso min: 0.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→44.09 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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