+Open data
-Basic information
Entry | Database: PDB / ID: 6ksy | ||||||
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Title | Crystal structure of arginase from Zymomonas mobilis ZM4 | ||||||
Components | Arginase/agmatinase/formiminoglutamase | ||||||
Keywords | HYDROLASE / arginase | ||||||
Function / homology | Ureohydrolase / Arginase family / Arginase family profile. / Ureohydrolase domain superfamily / hydrolase activity / metal ion binding / Arginase/agmatinase/formiminoglutamase Function and homology information | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.649 Å | ||||||
Authors | Park, S.Y. / Hwangbo, S.A. | ||||||
Citation | Journal: Front Microbiol / Year: 2019 Title: Characterization of a Dimeric Arginase FromZymomonas mobilisZM4. Authors: Hwangbo, S.A. / Kim, J.W. / Jung, S.J. / Jin, K.S. / Lee, J.O. / Kim, J.S. / Park, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ksy.cif.gz | 251 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ksy.ent.gz | 199.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ksy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ksy_validation.pdf.gz | 5.5 MB | Display | wwPDB validaton report |
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Full document | 6ksy_full_validation.pdf.gz | 5.5 MB | Display | |
Data in XML | 6ksy_validation.xml.gz | 48.1 KB | Display | |
Data in CIF | 6ksy_validation.cif.gz | 70.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/6ksy ftp://data.pdbj.org/pub/pdb/validation_reports/ks/6ksy | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 32154.740 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria) Strain: ATCC 31821 / ZM4 / CP4 / Gene: rocF, ZMO0432, ZMO1_ZMO0432 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NQE9 #2: Chemical | ChemComp-ZN / #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: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25 % (w/v) Polyethylene glycol 3350, 0.2 M Lithium Sulfate, 0.1 M Tris-HCl at pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2019 / Details: K-B |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 1.649→20 Å / Num. obs: 131592 / % possible obs: 95.2 % / Redundancy: 6.5 % / Rpim(I) all: 0.036 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.65→1.68 Å / Num. unique obs: 6498 / Rpim(I) all: 0.388 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.649→20 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.649→20 Å
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LS refinement shell | Resolution: 1.649→1.708 Å / Total num. of bins used: 1
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