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Yorodumi- PDB-4q3v: Crystal structure of Schistosoma mansoni arginase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q3v | ||||||
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Title | Crystal structure of Schistosoma mansoni arginase in complex with inhibitor BEC | ||||||
Components | Arginase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / arginase-deacetylase fold / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Schistosoma mansoni (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 2.7 Å | ||||||
Authors | Hai, Y. / Edwards, J.E. / Van Zandt, M.C. / Hoffmann, K.F. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Crystal Structure of Schistosoma mansoni Arginase, a Potential Drug Target for the Treatment of Schistosomiasis. Authors: Hai, Y. / Edwards, J.E. / Van Zandt, M.C. / Hoffmann, K.F. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q3v.cif.gz | 276.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q3v.ent.gz | 222.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q3v_validation.pdf.gz | 488.7 KB | Display | wwPDB validaton report |
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Full document | 4q3v_full_validation.pdf.gz | 499.5 KB | Display | |
Data in XML | 4q3v_validation.xml.gz | 49.9 KB | Display | |
Data in CIF | 4q3v_validation.cif.gz | 69 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3v ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3v | HTTPS FTP |
-Related structure data
Related structure data | 4q3pSC 4q3qC 4q3rC 4q3sC 4q3tC 4q3uC 4q40C 4q41C 4q42C 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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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42267.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: Smp_059980 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WVP6, arginase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56.04 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 4% v/v Tacsimate, pH 7.0, 12% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock double crystal sagittal focusing Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. all: 52114 / Num. obs: 51489 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.97 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.158 / Net I/σ(I): 10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: PHASER Starting model: PDB ENTRY 4Q3P Resolution: 2.7→49.477 Å / SU ML: 0.32 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.74 / 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 mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→49.477 Å
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Refine LS restraints |
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LS refinement shell |
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