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

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Basic information

Entry
Database: PDB / ID: 9sds
TitleStructure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and chloride at pH 5.5
Components
  • (Myeloperoxidase ...) x 2
  • Myeloperoxidase
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: 2.49 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
DepositionAug 14, 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
A: Myeloperoxidase light chain
E: Myeloperoxidase inhibitor SPIN
C: Myeloperoxidase
B: Myeloperoxidase light chain
D: Myeloperoxidase
F: Myeloperoxidase inhibitor SPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,52721
Polymers146,2456
Non-polymers5,28215
Water5,368298
1
A: Myeloperoxidase light chain
E: Myeloperoxidase inhibitor SPIN
C: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,88311
Polymers73,1223
Non-polymers2,7608
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myeloperoxidase light chain
D: Myeloperoxidase
F: Myeloperoxidase inhibitor SPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,64410
Polymers73,1223
Non-polymers2,5217
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.157, 111.157, 241.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Myeloperoxidase ... , 2 types, 4 molecules ABEF

#1: 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
#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 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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Protein , 1 types, 2 molecules CD

#3: Protein Myeloperoxidase / MPO


Mass: 53305.266 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, myeloperoxidase

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Sugars , 3 types, 6 molecules

#4: 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.: 2
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
#5: 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.: 3
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
#10: 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.: 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 , 5 types, 307 molecules

#6: 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
#7: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Na Acet 5.5 pH (Buffer) 10 %w/v PEG 1K (Precipitant) 7 %w/v PEG 8K (Precipitant) 0.4 M NaI (Salt)

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Data collection

DiffractionMean temperature: 213.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.9075 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 6, 2023 / Details: Vertical CRL/Horizontal Eliptical 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: 2.486→48.74 Å / Num. obs: 52854 / % possible obs: 97.7 % / Redundancy: 30.1 % / CC1/2: 0.972 / Rmerge(I) obs: 0.698 / Rpim(I) all: 0.134 / Rrim(I) all: 0.712 / Net I/σ(I): 8.7
Reflection shellResolution: 2.486→2.549 Å / Redundancy: 15.5 % / Rmerge(I) obs: 4.406 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2643 / CC1/2: 0.212 / Rpim(I) all: 1.152 / Rrim(I) all: 4.56 / % possible all: 69

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.74 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 20.378 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.569 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23391 2636 5 %RANDOM
Rwork0.1882 ---
obs0.19047 50178 98.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.49→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10022 0 333 298 10653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01210651
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3881.84814488
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4351243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.4885130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.345101739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.170.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028158
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8830.5714996
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5231.0256227
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4480.6895655
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.9866.1315667
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 152 -
Rwork0.325 2748 -
obs--74.8 %
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)
11.14920.1689-0.022.0257-0.30471.49020.04930.07320.0369-0.0086-0.0983-0.0115-0.05420.06140.0490.01420.01610.02750.06970.02530.08988.919315.697437.7757
26.51431.41950.10624.36391.0754.9552-0.14060.4383-0.2663-0.6632-0.0376-0.1710.25920.30330.17820.29970.08120.06890.33660.00950.254227.7197-8.690513.9888
30.951-0.08410.02681.5120.10341.22110.02910.0443-0.14010.0061-0.04220.07260.09280.00060.0130.0434-0.01310.0270.10470.02830.0736.65574.614137.4397
41.3123-0.31130.06782.4360.00951.53530.07820.15760.15340.0292-0.0664-0.0792-0.06110.1218-0.01170.03780.01050.06590.16670.07760.1453.363641.80217.9091
51.17610.1060.27461.67690.10561.1495-0.00130.17630.3545-0.00220.001-0.0962-0.23260.07270.00030.1070.03080.03140.17990.11730.2341.685352.81819.3545
63.39481.27251.53383.8805-0.36436.1203-0.08170.1250.27390.19530.1827-0.7027-0.13020.6661-0.10090.4358-0.0498-0.02920.63530.03370.924932.083665.706627.8563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A167 - 271
2X-RAY DIFFRACTION2E44 - 98
3X-RAY DIFFRACTION3C279 - 743
4X-RAY DIFFRACTION4B167 - 271
5X-RAY DIFFRACTION5D279 - 743
6X-RAY DIFFRACTION6F44 - 97

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