+Open data
-Basic information
Entry | Database: PDB / ID: 3mmr | ||||||
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Title | Structure of Plasmodium falciparum Arginase in complex with ABH | ||||||
Components | Arginase | ||||||
Keywords | HYDROLASE / malaria / ABH / LCR / parasite / L-arginine / boronic acid / metallohydrolase / binuclear / manganese | ||||||
Function / homology | Function and homology information Urea cycle / Neutrophil degranulation / arginase / arginine catabolic process to ornithine / arginase activity / urea cycle / manganese ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Dowling, D.P. / Ilies, M. / Olszewski, K.L. / Portugal, S. / Mota, M.M. / Llinas, M. / Christianson, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal structure of arginase from Plasmodium falciparum and implications for L-arginine depletion in malarial infection . Authors: Dowling, D.P. / Ilies, M. / Olszewski, K.L. / Portugal, S. / Mota, M.M. / Llinas, M. / 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 | 3mmr.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mmr.ent.gz | 62.3 KB | Display | PDB format |
PDBx/mmJSON format | 3mmr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/3mmr ftp://data.pdbj.org/pub/pdb/validation_reports/mm/3mmr | HTTPS FTP |
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-Related structure data
Related structure data | 1pq3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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 3D7 (eukaryote) / Strain: isolate 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-ABH / | #4: Chemical | ChemComp-BME / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.08 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.4 M Na/K Phosphate (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→49.354 Å / Num. all: 59546 / Num. obs: 31095 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.14→2.23 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.4 / Num. unique all: 3052 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1PQ3 Resolution: 2.14→37.112 Å / SU ML: 0.2 / Isotropic thermal model: isotropic / σ(F): 0.14 / Phase error: 17.45 / 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 / Bsol: 42.712 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.14→37.112 Å
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Refine LS restraints |
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LS refinement shell |
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