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Yorodumi- PDB-3sl0: Crystal Structure of P. falciparum arginase complexed with 2-amin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sl0 | ||||||
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Title | Crystal Structure of P. falciparum arginase complexed with 2-amino-6-borono-2-(difluoromethyl)hexanoic acid | ||||||
Components | Arginase | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / metallohydrolase / arginase fold / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Urea cycle / Neutrophil degranulation / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / manganese ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 Å | ||||||
Authors | Dowling, D.P. / Ilies, M. / Christianson, D.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Binding of alpha , alpha-disubstituted amino acids to arginase suggests new avenues for inhibitor design. Authors: Ilies, M. / Di Costanzo, L. / Dowling, D.P. / Thorn, K.J. / 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 | 3sl0.cif.gz | 144.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sl0.ent.gz | 112 KB | Display | PDB format |
PDBx/mmJSON format | 3sl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sl0_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 3sl0_full_validation.pdf.gz | 447.4 KB | Display | |
Data in XML | 3sl0_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3sl0_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/3sl0 ftp://data.pdbj.org/pub/pdb/validation_reports/sl/3sl0 | HTTPS FTP |
-Related structure data
Related structure data | 3gmzC 3gn0C 3sjtC 3skkC 3sl1C 3mmrS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 46452.039 Da / Num. of mol.: 1 / Fragment: UNP residues 22-411 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PFI0320w / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Codonplustm(de3) Ril / References: UniProt: Q8I384, arginase | ||||
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#2: Chemical | #3: Chemical | ChemComp-FB5 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.49 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.2 M Na/K Phosphate (8.0), VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.997→50 Å / Num. all: 38494 / Num. obs: 38494 / % possible obs: 99.9 % / Redundancy: 7.8 % / Rsym value: 0.09 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.997→2.07 Å / Redundancy: 7.8 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 3757 / Rsym value: 0.587 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MMR Resolution: 1.997→37.24 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.569 Å2 / ksol: 0.33 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.997→37.24 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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