+Open data
-Basic information
Entry | Database: PDB / ID: 6lug | ||||||
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Title | Crystal 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 / antibiotic biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 1.9 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 | 6lug.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lug.ent.gz | 94.8 KB | Display | PDB format |
PDBx/mmJSON format | 6lug.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6lug ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6lug | HTTPS FTP |
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-Related structure data
-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: 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: 38.98 % |
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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: 1.8924 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 18, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8924 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.1 Å / Num. obs: 35027 / % possible obs: 95.3 % / Redundancy: 12.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.03 / Rrim(I) all: 0.11 / Net I/σ(I): 19 / Num. measured all: 434720 / Scaling rejects: 614 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.288 / Num. unique obs: 1975 / CC1/2: 0.942 / Rpim(I) all: 0.131 / Rrim(I) all: 0.318 / % possible all: 79.2 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→44.1 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.07 / 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: 78.84 Å2 / Biso mean: 19.9904 Å2 / Biso min: 6.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→44.1 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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