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- PDB-7qzr: Structure of native leukocyte myeloperoxidase in complex with the... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qzr | |||||||||||||||
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Title | Structure of native leukocyte myeloperoxidase in complex with the Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus | |||||||||||||||
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![]() | OXIDOREDUCTASE / Phagocytosis Innate Immune Response Inhibitor Complex | |||||||||||||||
Function / homology | ![]() myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule ...myeloperoxidase / hypochlorous acid biosynthetic process / Events associated with phagocytolytic activity of PMN cells / phagocytic vesicle lumen / response to gold nanoparticle / response to yeast / respiratory burst involved in defense response / low-density lipoprotein particle remodeling / response to food / azurophil granule / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / defense response / peroxidase activity / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Pfanzagl, V. / Brito, J.A. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The staphylococcal inhibitory protein SPIN binds to human myeloperoxidase with picomolar affinity but only dampens halide oxidation. Authors: Leitgeb, U. / Furtmuller, P.G. / Hofbauer, S. / Brito, J.A. / Obinger, C. / Pfanzagl, V. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 779.3 KB | Display | ![]() |
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PDB format | ![]() | 653.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.8 MB | Display | ![]() |
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Full document | ![]() | 3.8 MB | Display | |
Data in XML | ![]() | 51 KB | Display | |
Data in CIF | ![]() | 73.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7z53C ![]() 5uzuS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACEF
#1: Protein | Mass: 12894.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: myeloperoxidase light chain / Source: (natural) ![]() #4: Protein | Mass: 11318.837 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: spn, BN1321_100004, BSG37_02260, BTN44_10620, DD547_00397, DQU54_02285, E3A28_06620, E3K14_02150, E4U00_13265, E5491_02175, ELP52_13680, EP54_01735, EQ90_14250, FA040_13280, G6X35_08925, G6X37_ ...Gene: spn, BN1321_100004, BSG37_02260, BTN44_10620, DD547_00397, DQU54_02285, E3A28_06620, E3K14_02150, E4U00_13265, E5491_02175, ELP52_13680, EP54_01735, EQ90_14250, FA040_13280, G6X35_08925, G6X37_02280, G6Y24_06940, GO788_14115, GO793_01255, GO814_02200, GO942_04205, GQX37_09010, GZ145_13040, HMPREF3211_00419, NCTC10654_00513, NCTC10702_00804, QU38_03305, RK64_02670, SAHC1335_03340, SAMEA1029536_02387, SAMEA103891420_01955, SAMEA103891454_02159, SAMEA2076468_01149, SAMEA2076503_02336, SAMEA2077334_02539, SAMEA2078260_02478, SAMEA2078588_01351, SAMEA2079501_02481, SAMEA2080344_01411, SAMEA2081063_02581, SAMEA4008569_02671, SAMEA70146418_02739 Production host: ![]() ![]() |
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-Myeloperoxidase heavy ... , 2 types, 2 molecules BD
#2: Protein | Mass: 53337.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: myeloperoxidase heavy chain / Source: (natural) ![]() |
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#3: Protein | Mass: 53337.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: myeloperoxidase heavy chain / Source: (natural) ![]() |
-Sugars , 2 types, 6 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 7 types, 538 molecules ![](data/chem/img/EDO.gif)
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#7: Chemical | ChemComp-EDO / #8: Chemical | #9: Chemical | #10: Chemical | #11: Chemical | ChemComp-PO4 / | #12: Chemical | ChemComp-PEG / | #13: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 8% (w/V) PEG 20000, 0.1 M BICINE pH 9, 0.5% (V/V) Dioxane |
-Data collection
Diffraction | Mean temperature: 213.15 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Nov 18, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.18→19.814 Å / Num. obs: 68945 / % possible obs: 92.9 % / Redundancy: 7.63 % Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary! CC1/2: 0.988 / CC1/2 anomalous: -0.08 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.1049 / Rrim(I) all: 0.2998 / AbsDiff over sigma anomalous: 0.728 / Baniso tensor eigenvalue 1: 23 Å2 / Baniso tensor eigenvalue 2: 23 Å2 / Baniso tensor eigenvalue 3: 38.4 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 2.179 Å / Aniso diffraction limit 2: 2.179 Å / Aniso diffraction limit 3: 2.486 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.19 / Num. measured all: 525797 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 92.6 / % possible ellipsoidal: 92.9 / % possible ellipsoidal anomalous: 92.6 / % possible spherical: 82.4 / % possible spherical anomalous: 82 / Redundancy anomalous: 4 / Signal type: local Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UZU Resolution: 2.18→19.81 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.336 / SU Rfree Blow DPI: 0.228
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Displacement parameters | Biso mean: 32.35 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.18→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.18→2.26 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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