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- PDB-8ogi: Structure of native human eosinophil peroxidase -

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Basic information

Entry
Database: PDB / ID: 8ogi
TitleStructure of native human eosinophil peroxidase
Components(Eosinophil peroxidase ...) x 2
KeywordsOXIDOREDUCTASE / hydrogen peroxide-dependent heme peroxidase immune system eosinophiles
Function / homology
Function and homology information


eosinophil migration / defense response to nematode / negative regulation of interleukin-5 production / negative regulation of macrophage cytokine production / lactoperoxidase activity / peroxidase / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / hydrogen peroxide catabolic process / peroxidase activity ...eosinophil migration / defense response to nematode / negative regulation of interleukin-5 production / negative regulation of macrophage cytokine production / lactoperoxidase activity / peroxidase / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / hydrogen peroxide catabolic process / peroxidase activity / secretory granule lumen / response to oxidative stress / defense response to bacterium / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily
Similarity search - Domain/homology
ACETATE ION / CITRATE ANION / HEME B/C / Eosinophil peroxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.547 Å
AuthorsPfanzagl, V. / Obinger, C.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP33997 Austria
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Posttranslational modification and heme cavity architecture of human eosinophil peroxidase-insights from first crystal structure and biochemical characterization.
Authors: Pfanzagl, V. / Gruber-Grunwald, C. / Leitgeb, U. / Furtmuller, P.G. / Obinger, C.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eosinophil peroxidase light chain
B: Eosinophil peroxidase heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,45124
Polymers65,5282
Non-polymers2,92322
Water8,503472
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17970 Å2
ΔGint-88 kcal/mol
Surface area22150 Å2
Unit cell
Length a, b, c (Å)53.123, 85.562, 139.395
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Eosinophil peroxidase ... , 2 types, 2 molecules AB

#1: Protein Eosinophil peroxidase light chain


Mass: 12025.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P11678
#2: Protein Eosinophil peroxidase heavy chain


Mass: 53501.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P11678

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Sugars , 2 types, 2 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 492 molecules

#4: Chemical ChemComp-HEB / HEME B/C / HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#11: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Trisodium Citrate, pH 4.1, 20 % (w/V) PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.547→42.937 Å / Num. obs: 92624 / % possible obs: 99.1 % / Redundancy: 9.09 %
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: 0.996 / CC1/2 anomalous: -0.363 / Rmerge(I) obs: 0.1103 / Rpim(I) all: 0.0378 / Rrim(I) all: 0.1169 / AbsDiff over sigma anomalous: 0.648 / Net I/σ(I): 9.94 / Num. measured all: 842329 / % possible anomalous: 99 / Redundancy anomalous: 4.76
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
4.199-42.9378.720.061528.214355043550499349930.996-0.4640.02170.06540.5311004.9100
3.333-4.1999.580.062827.854393543935458545850.993-0.4660.02110.06640.52395.75.1495.9
2.912-3.3339.380.073623.44447344473474047400.997-0.3630.02470.07780.631004.99100
2.646-2.9128.890.085619.234184241842470647060.996-0.2330.02950.09070.6541004.69100
2.456-2.6469.40.097817.014406644066468646860.995-0.2020.03270.10330.6691004.94100
2.311-2.4569.630.116814.84501745017467346730.993-0.2350.03860.12330.6811005.04100
2.195-2.3119.720.140712.784541845418467546750.991-0.1670.04640.14840.6811005.07100
2.1-2.1959.760.176210.454535445354464746470.988-0.1510.0580.18580.6841005.08100
2.019-2.19.140.21458.64271042710467146710.984-0.0930.07330.22710.7021004.76100
1.949-2.0198.910.27056.814130541305463746370.97-0.0720.09390.28690.68599.94.63100
1.888-1.9499.230.34655.494271142711462846280.958-0.0590.11830.36680.69299.94.8100
1.834-1.8889.450.41054.524385143851463946390.941-0.0370.13860.43420.6761004.9100
1.786-1.8349.570.49623.754450244502465146510.92-0.0380.16650.52440.66499.94.96100
1.743-1.7869.630.60833.054440144401461346130.88-0.0480.2040.64290.63899.94.9999.9
1.703-1.7439.670.72832.584460244602461446140.846-0.0260.24410.76960.6431005100
1.667-1.7039.670.89092.14468944689462146210.778-0.0310.29870.94160.6421004.99100
1.633-1.6679.131.07561.674239842398464246420.691-0.0320.37181.1410.6351004.72100
1.603-1.6338.161.26591.323736037360457845780.557-0.0050.46581.3540.63999.94.21100
1.574-1.6037.371.49261.063302633026448444840.438-0.0350.5791.60830.62396.83.897
1.547-1.5746.551.69430.862711927119414141410.377-0.0050.69791.84190.64188.53.489.7

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20221121data processing
XDSJan 10, 2022data reduction
Aimless0.7.9data scaling
TRUNCATE8.0.006data processing
BUSTER2.10.4refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.547→22.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.069
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 4700 -RANDOM
Rwork0.174 ---
obs0.1746 92291 98.8 %-
Displacement parametersBiso mean: 27.48 Å2
Baniso -1Baniso -2Baniso -3
1-1.1713 Å20 Å20 Å2
2--3.6272 Å20 Å2
3----4.7985 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.547→22.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4607 0 191 472 5270
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019969HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9717934HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3050SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1632HARMONIC5
X-RAY DIFFRACTIONt_it5047HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion618SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9977SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.26
X-RAY DIFFRACTIONt_other_torsion14.58
LS refinement shellResolution: 1.55→1.56 Å
RfactorNum. reflection% reflection
Rfree0.3835 110 -
Rwork0.3352 --
obs0.3381 1846 80.93 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5605-0.09610.1410.2981-0.08870.2125-0.02550.0247-0.02310.0247-0.0004-0.0154-0.0231-0.01540.0259-0.0118-0.0005-0.0062-0.0274-0.0018-0.00639.0541-0.4608-18.3719
20.64680.00920.1570.2553-0.0560.2646-0.0165-0.0193-0.0172-0.01930.0050.0258-0.01720.02580.0115-0.0091-0.00040.0042-0.04510.0053-0.00086.786-4.1694-29.4208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|* }B251 - 715
2X-RAY DIFFRACTION1{ B|* }B1000 - 4017
3X-RAY DIFFRACTION2{ A|* }A140 - 243

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