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- PDB-9qj3: Structure of native leukocyte myeloperoxidase in complex with a t... -

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Basic information

Entry
Database: PDB / ID: 9qj3
TitleStructure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and iodide at pH 5.5
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 / IODIDE ION / Myeloperoxidase / Myeloperoxidase inhibitor SPIN
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 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 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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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
A: Myeloperoxidase light chain
C: Myeloperoxidase light chain
E: Myeloperoxidase inhibitor SPIN
F: Myeloperoxidase inhibitor SPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,737105
Polymers146,2776
Non-polymers16,46099
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.361, 111.361, 242.068
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-999-

HOH

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Components

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Myeloperoxidase ... , 3 types, 6 molecules BDACEF

#1: Protein Myeloperoxidase heavy chain


Mass: 53321.270 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 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
#3: 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 Staphyloccal Peroxidase Inhibitor SPIN from Staphylococcus aureus
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SAOUHSC_00401 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2G0X2

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Sugars , 3 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.: 4
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)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose-(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: 1098.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DGlcpNAcb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-1-2-2-3/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-GlcpNAc]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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

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Non-polymers , 4 types, 366 molecules

#7: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: I
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 47.19 % / Description: Rhomboid
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Na Acet 5.5 pH 6 %(w/v) PEG 8K 10 %(w/v) PEG 1K 0.4 M NaI

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Data collection

DiffractionMean temperature: 213.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.9075 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: 1.9075 Å / Relative weight: 1
ReflectionResolution: 2.63→101.17 Å / Num. obs: 38848 / % possible obs: 93.8 % / Redundancy: 11.5 % / CC1/2: 0.931 / Rmerge(I) obs: 0.343 / Rpim(I) all: 0.105 / Rrim(I) all: 0.359 / Net I/σ(I): 6.9
Reflection shellResolution: 2.63→2.81 Å / Rmerge(I) obs: 2.538 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1942 / CC1/2: 0.578 / Rpim(I) all: 0.782 / Rrim(I) all: 2.657 / % possible all: 55.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→101.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.288 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1925 5 %RANDOM
Rwork0.19217 ---
obs0.19498 36923 84.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.555 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---0.58 Å20 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.63→101.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10077 0 434 273 10784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01210719
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169985
X-RAY DIFFRACTIONr_angle_refined_deg1.8091.84814603
X-RAY DIFFRACTIONr_angle_other_deg0.6031.76722977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.58851252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.8025131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.689101748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.21603
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022617
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0862.2495020
X-RAY DIFFRACTIONr_mcbond_other2.0862.2495020
X-RAY DIFFRACTIONr_mcangle_it3.3644.0386265
X-RAY DIFFRACTIONr_mcangle_other3.3634.0386266
X-RAY DIFFRACTIONr_scbond_it2.7052.4755699
X-RAY DIFFRACTIONr_scbond_other2.7052.4755700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3634.4668338
X-RAY DIFFRACTIONr_long_range_B_refined6.73827.9743695
X-RAY DIFFRACTIONr_long_range_B_other6.73227.8943648
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.635→2.703 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 15 -
Rwork0.217 227 -
obs--7.29 %
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)
11.0164-0.07110.05961.37920.19031.23520.06510.0088-0.11390.0089-0.02610.05520.1432-0.0262-0.0390.1169-0.03220.00980.15830.02580.02776.71164.569737.7367
21.00230.03620.24161.59250.12430.9084-0.03320.08470.3774-0.10210.0022-0.0963-0.28080.07920.0310.20160.00890.0360.22930.09820.19631.694953.090219.2689
31.51960.21380.4731.6788-0.42691.89340.07780.07270.0462-0.0127-0.14360.00580.03910.070.06580.0338-0.0090.02780.09680.00810.02949.026415.751737.9757
41.7814-0.21910.36192.13990.14341.56590.06850.13760.2246-0.1278-0.0866-0.1771-0.15630.18970.01810.12510.00310.0840.16480.08280.10483.53441.94117.9435
56.50790.63210.51974.8508-0.06114.31450.09670.3576-0.3776-0.3199-0.0128-0.45810.17330.4997-0.08390.35310.09580.05150.39940.0310.199228.3754-8.79813.986
61.90070.8250.60171.24840.20670.3316-0.25130.02580.2283-0.13610.2516-0.2731-0.17720.3554-0.00030.9165-0.14410.02131.1468-0.01511.269532.776966.426227.4231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B279 - 800
2X-RAY DIFFRACTION2D279 - 798
3X-RAY DIFFRACTION3A167 - 271
4X-RAY DIFFRACTION4C167 - 271
5X-RAY DIFFRACTION5E43 - 99
6X-RAY DIFFRACTION6F43 - 100

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