+Open data
-Basic information
Entry | Database: PDB / ID: 7oqr | ||||||
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Title | Crystal structure of Trypanosoma cruzi peroxidase | ||||||
Components | Ascorbate peroxidase | ||||||
Keywords | OXIDOREDUCTASE / heme peroxidase | ||||||
Function / homology | Function and homology information L-ascorbate peroxidase / L-ascorbate peroxidase activity / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Freeman, S.L. / Kwon, H. / Skafar, V. / Fielding, A.J. / Martinez, A. / Piacenza, L. / Radi, R. / Raven, E.L. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2022 Title: Crystal structure of Trypanosoma cruzi heme peroxidase and characterization of its substrate specificity and compound I intermediate. Authors: Freeman, S.L. / Skafar, V. / Kwon, H. / Fielding, A.J. / Moody, P.C.E. / Martinez, A. / Issoglio, F.M. / Inchausti, L. / Smircich, P. / Zeida, A. / Piacenza, L. / Radi, R. / Raven, E.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oqr.cif.gz | 139 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oqr.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 7oqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/7oqr ftp://data.pdbj.org/pub/pdb/validation_reports/oq/7oqr | HTTPS FTP |
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-Related structure data
Related structure data | 7optSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36511.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: APX, C3747_335g5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I1N3, L-ascorbate peroxidase |
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-Non-polymers , 7 types, 442 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-OXY / | #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2019 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.76→29.28 Å / Num. obs: 76005 / % possible obs: 99.8 % / Redundancy: 20 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 22.5 | |||||||||||||||
Reflection shell | Resolution: 1.76→1.8 Å / Rmerge(I) obs: 0.785 / Num. unique obs: 4170 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7OPT Resolution: 1.76→29.28 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.274 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.36 Å2 / Biso mean: 25.733 Å2 / Biso min: 15.17 Å2
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Refinement step | Cycle: final / Resolution: 1.76→29.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.762→1.808 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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