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Yorodumi- PDB-4q3r: Crystal structure of Schistosoma mansoni arginase in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q3r | ||||||
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Title | Crystal structure of Schistosoma mansoni arginase in complex with inhibitor ABHDP | ||||||
Components | (Arginase) x 2 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.169 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 | 4q3r.cif.gz | 287.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q3r.ent.gz | 227.1 KB | Display | PDB format |
PDBx/mmJSON format | 4q3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q3r_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4q3r_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4q3r_validation.xml.gz | 54 KB | Display | |
Data in CIF | 4q3r_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/4q3r ftp://data.pdbj.org/pub/pdb/validation_reports/q3/4q3r | HTTPS FTP |
-Related structure data
Related structure data | 4q3pSC 4q3qC 4q3sC 4q3tC 4q3uC 4q3vC 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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3 |
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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
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 42283.293 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 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: Protein | Mass: 42267.293 Da / Num. of mol.: 2 / Fragment: SEE REMARK 999 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 |
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-Non-polymers , 7 types, 661 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-CS / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-XA2 / ( #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE PRESENCE IN THE ASYMMETRIC UNIT OF TWO PROTEINS WITH DISTINCT PATTERNS OF SIDE CHAIN ...THE PRESENCE IN THE ASYMMETRIC |
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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: 2.76 Å3/Da / Density % sol: 55.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.15 M cesium chloride, 13% w/v PEG3350, pH 8.5, 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: Mar 24, 2014 / 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: 2.169→50 Å / Num. all: 98198 / Num. obs: 96529 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.7 % / Biso Wilson estimate: 23.78 Å2 / Rmerge(I) obs: 0.165 / Rsym value: 0.165 / Net I/σ(I): 11.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4Q3P Resolution: 2.169→49.226 Å / SU ML: 0.2 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.2 / 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: 32.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.169→49.226 Å
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Refine LS restraints |
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LS refinement shell |
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