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- PDB-9qex: Structure of native leukocyte myeloperoxidase in complex with a t... -

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Basic information

Entry
Database: PDB / ID: 9qex
TitleStructure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and thiocyanate at pH 7.5
Components(Myeloperoxidase ...) x 3
KeywordsOXIDOREDUCTASE / Innate immunity / enzyme substrate complex / inhibitor
Function / homology
Function and homology information


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 / azurophil granule / response to food ...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 / azurophil granule / response to food / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / chromatin binding / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
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
PROTOPORPHYRIN IX CONTAINING FE / THIOCYANATE ION / Myeloperoxidase / Myeloperoxidase inhibitor SPIN
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsLeitgeb, U. / Pfanzagl, V.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundP33997 Austria
Austrian Science FundW1224 Austria
CitationJournal: Int.J.Biol.Macromol. / Year: 2025
Title: Halide binding by myeloperoxidase is regulated by access channel dynamics and charge interactions.
Authors: Leitgeb, U. / Crha, R. / Fegerl, I. / Furtmuller, P.G. / Oostenbrink, C. / Pfanzagl, V.
History
DepositionMar 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Myeloperoxidase heavy chain
D: Myeloperoxidase heavy chain
E: Myeloperoxidase inhibitor SPIN
F: Myeloperoxidase inhibitor SPIN
A: Myeloperoxidase light chain
C: Myeloperoxidase light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,10231
Polymers146,3096
Non-polymers5,79325
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40480 Å2
ΔGint-165 kcal/mol
Surface area45680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.328, 111.328, 242.725
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
32E
42F
53A
63C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNARGARGBA280 - 7422 - 464
211ASNASNARGARGDB280 - 7422 - 464
322ALAALALYSLYSEC43 - 971 - 55
422ALAALALYSLYSFD43 - 971 - 55
533CYSCYSALAALAAE167 - 2713 - 107
633CYSCYSALAALACF167 - 2713 - 107

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

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Components

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Myeloperoxidase ... , 3 types, 6 molecules BDEFAC

#1: Protein Myeloperoxidase heavy chain


Mass: 53337.266 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Heavy chain of myeloperoxidase / Source: (natural) Homo sapiens (human) / References: UniProt: P05164
#2: Protein Myeloperoxidase inhibitor SPIN


Mass: 6922.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: A truncated version of the staphylococcal peroxidase inhibitor SPIN aureus
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAOUHSC_00401 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G0X2
#3: Protein Myeloperoxidase light chain


Mass: 12894.465 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 167-271 / Source method: isolated from a natural source / Details: Light chain of Myeloperoxidase / Source: (natural) Homo sapiens (human) / References: UniProt: P05164

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Sugars , 4 types, 6 molecules

#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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 , 4 types, 794 molecules

#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CNS
#10: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.3 % / Description: Rhomboid
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M TRIS 7.5 pH (Buffer) 4 %(w/v) PEG 8K (Precipitant) 10 %(w/v) PEG 1K (Precipitant) 0.4 M KSCN (Salt)

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Data collection

DiffractionMean temperature: 213.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2023 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.9→101.192 Å / Num. obs: 86444 / % possible obs: 93.3 % / Redundancy: 9.1 % / CC1/2: 0.977 / Rmerge(I) obs: 0.256 / Rpim(I) all: 0.09 / Rrim(I) all: 0.272 / Net I/σ(I): 6.7
Reflection shellResolution: 1.9→2.101 Å / Redundancy: 7.7 % / Rmerge(I) obs: 3.456 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4322 / CC1/2: 0.241 / Rpim(I) all: 1.372 / Rrim(I) all: 3.729 / % possible all: 66.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.903→101.192 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.169 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.172
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 4245 4.911 %RANDOM
Rwork0.1682 82195 --
all0.171 ---
obs-86440 72.106 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.466 Å2
Baniso -1Baniso -2Baniso -3
1--0.128 Å20 Å20 Å2
2---0.128 Å20 Å2
3---0.255 Å2
Refinement stepCycle: LAST / Resolution: 1.903→101.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10063 0 373 775 11211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01210709
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169947
X-RAY DIFFRACTIONr_angle_refined_deg2.0091.84714552
X-RAY DIFFRACTIONr_angle_other_deg0.661.76622884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.86551250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.0655130
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.77952
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.04101743
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.75910518
X-RAY DIFFRACTIONr_chiral_restr0.0920.21589
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212811
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022609
X-RAY DIFFRACTIONr_nbd_refined0.2550.22259
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.29466
X-RAY DIFFRACTIONr_nbtor_refined0.1810.25284
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.25644
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2633
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1320.26
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.245
X-RAY DIFFRACTIONr_nbd_other0.190.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5420.247
X-RAY DIFFRACTIONr_mcbond_it2.1042.0635030
X-RAY DIFFRACTIONr_mcbond_other2.1042.0635030
X-RAY DIFFRACTIONr_mcangle_it2.963.6896260
X-RAY DIFFRACTIONr_mcangle_other2.963.696261
X-RAY DIFFRACTIONr_scbond_it3.1962.4185679
X-RAY DIFFRACTIONr_scbond_other3.1962.4185680
X-RAY DIFFRACTIONr_scangle_it4.7254.3278292
X-RAY DIFFRACTIONr_scangle_other4.7244.3278293
X-RAY DIFFRACTIONr_lrange_it6.426.37643720
X-RAY DIFFRACTIONr_lrange_other6.35126.11343143
X-RAY DIFFRACTIONr_ncsr_local_group_10.0820.0515342
X-RAY DIFFRACTIONr_ncsr_local_group_20.1470.051621
X-RAY DIFFRACTIONr_ncsr_local_group_30.1070.052870
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.0820.05008
12DX-RAY DIFFRACTIONLocal ncs0.0820.05008
23EX-RAY DIFFRACTIONLocal ncs0.147140.05007
24FX-RAY DIFFRACTIONLocal ncs0.147140.05007
35AX-RAY DIFFRACTIONLocal ncs0.106810.05008
36CX-RAY DIFFRACTIONLocal ncs0.106810.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.903-1.9530.302170.2843020.28587580.9370.9173.64240.267
1.953-2.0060.246440.2578130.25684950.960.94910.08830.242
2.006-2.0640.282920.27716120.27783030.9350.93920.52270.265
2.064-2.1280.3171370.28625670.28780740.8890.81133.49020.265
2.128-2.1980.2732370.24446400.24677920.9510.95862.58980.229
2.198-2.2750.2653370.23868130.23975970.9540.95794.11610.221
2.275-2.3610.2673690.21169520.21473210.9530.971000.193
2.361-2.4570.2243330.18767150.18870480.9680.9791000.168
2.457-2.5660.253270.17164340.17567610.9640.9821000.153
2.566-2.6910.2223200.1761540.17364740.970.9791000.153
2.691-2.8370.2163160.1658890.16362050.9730.9851000.146
2.837-3.0090.2272950.16155780.16458740.9680.98499.9830.151
3.009-3.2160.2162660.16852500.1755200.9690.98399.92750.162
3.216-3.4730.2051970.16740120.16951630.9770.98481.52240.164
3.473-3.8050.2211940.15439970.15747640.9750.98887.97230.157
3.805-4.2530.1682050.13137940.13343610.9860.98991.69920.14
4.253-4.9090.1721640.12436670.12538550.9840.99299.37740.141
4.909-6.0090.1851700.14631040.14833020.9830.9999.1520.165
6.009-8.4830.2131400.16724560.1726230.9750.98498.97060.193
8.483-101.1920.22850.19714470.19815620.9210.96998.07940.25
Refinement TLS params.

Method: refined / 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)
10.59730.0043-0.06070.95810.12080.92330.01840.00990.0978-0.016-0.01860.0268-0.1443-0.01620.00020.05780.0157-0.01470.06170.01710.0336.7053-4.305222.5981
20.7705-0.0978-0.07951.120.02560.8239-0.02-0.0451-0.27340.04330.0021-0.06780.27160.01010.01790.123-0.0193-0.01910.10760.04840.1551.4088-53.188741.6216
33.0527-1.30260.72333.74450.00763.8038-0.0431-0.04570.28420.17170.0346-0.2899-0.17030.3050.00850.1804-0.0605-0.03760.1725-0.01250.133727.93518.575646.6895
41.1922-0.2943-0.28610.13430.21291.08550.117-0.036-0.1649-0.06270.056-0.17620.30430.3208-0.17290.76230.07690.05360.7405-0.02841.006832.4259-66.417432.9671
50.8635-0.0149-0.05471.151-0.19131.31510.0273-0.0482-0.05040.0279-0.0583-0.0126-0.00780.04570.0310.01020.0029-0.01130.04340.00440.0158.8535-15.806422.5929
61.15660.2013-0.03471.4060.02121.4272-0.0016-0.1087-0.18040.04-0.0308-0.08630.10160.12070.03230.04110.0092-0.03660.07820.04720.08723.2656-41.887142.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLB280 - 744
2X-RAY DIFFRACTION2ALLD279 - 743
3X-RAY DIFFRACTION3ALLE43 - 98
4X-RAY DIFFRACTION4ALLF43 - 100
5X-RAY DIFFRACTION5ALLA167 - 271
6X-RAY DIFFRACTION6ALLC167 - 271

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