+Open data
-Basic information
Entry | Database: PDB / ID: 5amm | ||||||
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Title | Structure of Leishmania major peroxidase D211N mutant | ||||||
Components | ASCORBATE PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information iodide peroxidase activity / L-ascorbate oxidase activity / L-ascorbate peroxidase activity / stabilization of membrane potential / cytochrome-c peroxidase / cytochrome-c peroxidase activity / cytochrome-c oxidase activity / calcium ion homeostasis / reactive oxygen species metabolic process / response to reactive oxygen species ...iodide peroxidase activity / L-ascorbate oxidase activity / L-ascorbate peroxidase activity / stabilization of membrane potential / cytochrome-c peroxidase / cytochrome-c peroxidase activity / cytochrome-c oxidase activity / calcium ion homeostasis / reactive oxygen species metabolic process / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / cellular response to oxidative stress / mitochondrial matrix / heme binding / negative regulation of apoptotic process / metal ion binding Similarity search - Function | ||||||
Biological species | LEISHMANIA MAJOR (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å | ||||||
Authors | Chreifi, G. / Fields, J.B. / Hollingsworth, S.A. / Heyden, M. / Arce, A.P. / Magana-Garcia, H.I. / Poulos, T.L. / Tobias, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2015 Title: "Bind and Crawl" Association Mechanism of Leishmania Major Peroxidase and Cytochrome C Revealed by Brownian and Molecular Dynamics Simulations. Authors: Fields, J.B. / Hollingsworth, S.A. / Chreifi, G. / Heyden, M. / Arce, A.P. / Magana-Garcia, H.I. / Poulos, T.L. / Tobias, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5amm.cif.gz | 230.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amm.ent.gz | 186.9 KB | Display | PDB format |
PDBx/mmJSON format | 5amm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5amm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5amm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5amm_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 5amm_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amm ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amm | HTTPS FTP |
-Related structure data
Related structure data | 3rivS 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
#1: Protein | Mass: 30593.740 Da / Num. of mol.: 2 / Fragment: C-TERMINAL CATALYTIC DOMAIN, RESIDUES 35-303 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q4Q3K2, L-ascorbate peroxidase, cytochrome-c peroxidase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THE PROTEIN EXPRESSED IS DELTA34LMP, WHICH HAD THE FIRST 34 RESIDUES REMOVED. | |
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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: 2.39 Å3/Da / Density % sol: 48.56 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 10% PEG MME 5000, 0.1M MES:NAOH PH 6.5, 7.5 MM PRASEODYMIUM(III) ACETATE HYDRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.0798 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2013 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0798 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 34997 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.69 |
Reflection shell | Resolution: 2.09→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.35 / % possible all: 94.9 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RIV Resolution: 2.09→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 13.605 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED RESIDUES 301-303 ARE DISORDERED IN BOTH CHAINS.
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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 mean: 65.359 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→50 Å
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Refine LS restraints |
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