+Open data
-Basic information
Entry | Database: PDB / ID: 5via | ||||||
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Title | Crystal structural of Leishmania major pseudoperoxidase | ||||||
Components | Pseudoperoxidase | ||||||
Keywords | OXIDOREDUCTASE / heme protein / peroxidase | ||||||
Function / homology | Function and homology information response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / membrane => GO:0016020 / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Leishmania major (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.764 Å | ||||||
Authors | Chreifi, G. / Dejam, D. / Poulos, T.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Inorg. Chem. / Year: 2017 Title: Crystal structure and functional analysis of Leishmania major pseudoperoxidase. Authors: Chreifi, G. / Dejam, D. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5via.cif.gz | 129.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5via.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 5via.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/5via ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5via | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33066.293 Da / Num. of mol.: 1 / Fragment: UNP residues 49-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_21_1567 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4QC30 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 14 mg/mL protein, 5% 2-methyl-2,4-pentanediol, 10% polyethylene glycol 6000, and 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076 Å |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Dec 16, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18076 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→48.88 Å / Num. obs: 31236 / % possible obs: 98.22 % / Redundancy: 18 % / Biso Wilson estimate: 34.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.049 / Net I/σ(I): 73.11 |
Reflection shell | Resolution: 1.76→1.83 Å / Redundancy: 16.5 % / Num. unique obs: 3100 / CC1/2: 0.297 / % possible all: 94.03 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.764→48.875 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.764→48.875 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 32.8372 Å / Origin y: 41.2282 Å / Origin z: 60.1489 Å
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Refinement TLS group | Selection details: (chain A and resid 56:333) |