PDB-9qe3: Structure of native leukocyte myeloperoxidase in complex with a t...

ID or keywords:

Entry

Database: PDB / ID: 9qe3

Title

Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate at pH 5.5

Components

(Myeloperoxidase ...) x 3

Keywords

OXIDOREDUCTASE / 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 ...
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.06 Å

Authors

Leitgeb, U. / Pfanzagl, V.

Funding support

Austria, 2items

Citation

Journal: 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

Deposition	Mar 7, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 15, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9qe3.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9qe3.ent.gz	818 KB	Display	PDB format
PDBx/mmJSON format	9qe3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9qe3_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	9qe3_full_validation.pdf.gz	2 MB	Display
Data in XML	9qe3_validation.xml.gz	60.5 KB	Display
Data in CIF	9qe3_validation.cif.gz	79.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qe/9qe3 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/9qe3	HTTPS FTP

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Related structure data

Related structure data	9qexC 9qgaC 9qj3C 9qjoC 9sdsC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#17 - May 2001 Cyclooxygenase similarity (5)

Deposited unit

E: Myeloperoxidase inhibitor SPIN

F: Myeloperoxidase inhibitor SPIN

A: Myeloperoxidase light chain

C: Myeloperoxidase light chain

B: Myeloperoxidase heavy chain

D: Myeloperoxidase heavy chain

hetero molecules

154 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: surface plasmon resonance

Unit cell

Length a, b, c (Å)	110.507, 110.507, 241.574
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	E
2	1	F
3	2	A
4	2	C
5	3	B
6	3	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	TYR	TYR	E	A	46 - 101	1 - 56
2	1	1	ALA	ALA	TYR	TYR	F	B	46 - 101	1 - 56
3	2	2	CYS	CYS	ALA	ALA	A	C	167 - 271	3 - 107
4	2	2	CYS	CYS	ALA	ALA	C	D	167 - 271	3 - 107
5	3	3	ASN	ASN	ARG	ARG	B	E	280 - 742	2 - 464
6	3	3	ASN	ASN	ARG	ARG	D	F	280 - 742	2 - 464

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6

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Myeloperoxidase ... , 3 types, 6 molecules EFACBD

#1: 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
#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 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

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Sugars , 2 types, 6 molecules

#4: Polysaccharide

alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...

Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}	LINUCS	PDB-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.: 4 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 4 types, 439 molecules

#5: Chemical	... ChemComp-SEK / SELENOCYANATE ION Mass: 104.977 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: CNSe
#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
#8: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.31 Å³/Da / Density % sol: 46.75 % / Description: Rhomboid
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Na Acet 5.5 pH (Buffer) 6 %(w/v) PEG 8K (Precipitant) 10 %(w/v) PEG 1K (Precipitant) 0.4 M KSeCN (Salt)

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Data collection

Diffraction	Mean temperature: 213.15 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2023 / Details: Toroidal mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8856 Å / Relative weight: 1
Reflection	Resolution: 2.058→19.89 Å / Num. obs: 62476 / % possible obs: 94.3 % / Redundancy: 13.4 % / CC_1/2: 0.993 / R_merge(I) obs: 0.353 / R_pim(I) all: 0.1 / R_rim(I) all: 0.386 / Net I/σ(I): 2.3576
Reflection shell	Resolution: 2.058→2.303 Å / Redundancy: 13.4 % / R_merge(I) obs: 3.255 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3124 / CC_1/2: 0.54 / R_pim(I) all: 0.92 / R_rim(I) all: 3.384 / % possible all: 65.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
autoPROC		data reduction
STARANISO		data scaling
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.06→19.89 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.919 / SU B: 10.052 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2342	3150	5.042 %	RANDOM
R_work	0.1788	59321	-	-
all	0.182	-	-	-
obs	-	62471	68.404 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 39.025 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.008 Å²	-0 Å²	-0 Å²
2-	-	-0.008 Å²	-0 Å²
3-	-	-	0.016 Å²

Refinement step

Cycle: LAST / Resolution: 2.06→19.89 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10063	0	360	403	10826

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.012	10695
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	9907
X-RAY DIFFRACTION	r_angle_refined_deg	1.904	1.85	14476
X-RAY DIFFRACTION	r_angle_other_deg	0.738	1.767	22779
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.47	5	1248
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.644	5	130
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.486	5	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.631	10	1743
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.041	10	519
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	1568
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12780
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	2604
X-RAY DIFFRACTION	r_nbd_refined	0.195	0.2	2185
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.155	0.2	9685
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	5252
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	5830
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.136	0.2	484
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.059	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.133	0.2	31
X-RAY DIFFRACTION	r_nbd_other	0.103	0.2	99
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.156	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	2.2	2.526	5050
X-RAY DIFFRACTION	r_mcbond_other	2.192	2.523	5037
X-RAY DIFFRACTION	r_mcangle_it	3.371	4.535	6252
X-RAY DIFFRACTION	r_mcangle_other	3.371	4.535	6253
X-RAY DIFFRACTION	r_scbond_it	2.68	2.716	5645
X-RAY DIFFRACTION	r_scbond_other	2.68	2.717	5646
X-RAY DIFFRACTION	r_scangle_it	4.146	4.904	8224
X-RAY DIFFRACTION	r_scangle_other	4.145	4.905	8225
X-RAY DIFFRACTION	r_lrange_it	5.698	25.606	11923
X-RAY DIFFRACTION	r_lrange_other	5.693	25.612	11881
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.113	0.05	1684
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	2832
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.08	0.05	15390

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	E	X-RAY DIFFRACTION	Local ncs	0.11319	0.05007
1	2	F	X-RAY DIFFRACTION	Local ncs	0.11319	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.09605	0.05007
2	4	C	X-RAY DIFFRACTION	Local ncs	0.09605	0.05007
3	5	B	X-RAY DIFFRACTION	Local ncs	0.07962	0.05008
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07962	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.06-2.113	0.274	5	0.204	54	X-RAY DIFFRACTION	1.19
2.113-2.17	0.3	18	0.217	374	X-RAY DIFFRACTION	5.9729
2.17-2.232	0.267	61	0.218	839	X-RAY DIFFRACTION	14.1643
2.232-2.3	0.322	76	0.233	1589	X-RAY DIFFRACTION	26.8765
2.3-2.374	0.306	128	0.232	2258	X-RAY DIFFRACTION	39.7137
2.374-2.457	0.29	152	0.22	2816	X-RAY DIFFRACTION	50.7437
2.457-2.548	0.257	255	0.226	4388	X-RAY DIFFRACTION	82.5569
2.548-2.65	0.302	299	0.225	4961	X-RAY DIFFRACTION	96.9585
2.65-2.766	0.27	269	0.21	4963	X-RAY DIFFRACTION	99.8855
2.766-2.898	0.25	232	0.202	4755	X-RAY DIFFRACTION	100
2.898-3.051	0.27	238	0.198	4543	X-RAY DIFFRACTION	100
3.051-3.231	0.265	228	0.2	4314	X-RAY DIFFRACTION	100
3.231-3.448	0.242	210	0.19	4070	X-RAY DIFFRACTION	99.9766
3.448-3.715	0.22	185	0.169	3826	X-RAY DIFFRACTION	100
3.715-4.055	0.191	188	0.147	3526	X-RAY DIFFRACTION	99.9731
4.055-4.511	0.173	154	0.132	3247	X-RAY DIFFRACTION	100
4.511-5.164	0.167	159	0.13	2879	X-RAY DIFFRACTION	100
5.164-6.221	0.233	122	0.163	2519	X-RAY DIFFRACTION	100
6.221-8.397	0.235	105	0.17	2032	X-RAY DIFFRACTION	100
8.397-19.89	0.246	66	0.181	1368	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.4264	1.305	-0.4072	3.1849	-0.3036	2.0753	0.0746	-0.1363	-0.2445	0.1236	-0.0439	-0.3364	0.3224	0.1807	-0.0307	0.1332	0.0478	-0.0165	0.129	0.0342	0.1386	8.614	-28.2028	-13.9391
2	1.1452	0.8564	-0.0381	0.8272	0.2846	0.6313	0.0305	-0.0286	-0.1234	0.1142	-0.0275	0.0496	0.2653	0.0377	-0.003	0.5131	-0.0193	-0.0367	0.505	-0.0149	0.7723	-66.2896	-32.3479	-27.7069
3	1.0264	0.1105	0.0308	0.72	0.0334	1.1367	-0.0444	-0.0102	0.0015	-0.0055	0.0314	0.0488	0.0207	-0.0322	0.013	0.0093	0.0013	0.0067	0.0108	0.0162	0.0308	-15.6949	-8.9779	-37.9979
4	0.9431	-0.1512	0.0711	0.9769	0.2446	0.8099	-0.046	-0.1011	-0.0672	0.0314	0.0365	0.1336	0.0371	-0.0748	0.0095	0.0337	-0.0025	0.0342	0.0608	0.049	0.0912	-41.7162	-3.5289	-17.9387
5	0.8669	-0.0504	0.1591	0.6076	0.0486	0.6588	-0.0162	0.0325	0.0389	-0.0286	0.027	-0.0872	-0.0232	0.0934	-0.0108	0.0391	-0.022	0.0126	0.0485	0.0108	0.0299	-4.5933	-6.6099	-37.7205
6	0.8524	0.0734	-0.0012	0.5995	0.0529	0.5311	-0.0105	-0.0796	-0.0488	0.0124	-0.0036	0.2212	0.0058	-0.1748	0.0141	0.062	0.0212	0.0299	0.1114	0.0322	0.1416	-52.8337	-1.5386	-19.2314

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	E	46 - 102
2	X-RAY DIFFRACTION	2	ALL	F	46 - 103
3	X-RAY DIFFRACTION	3	ALL	A	167 - 271
4	X-RAY DIFFRACTION	4	ALL	C	167 - 271
5	X-RAY DIFFRACTION	5	ALL	B	556 - 744
6	X-RAY DIFFRACTION	6	ALL	D	556 - 743

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Myeloperoxidase ... , 3 types, 6 molecules EFACBD

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Non-polymers , 4 types, 439 molecules

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-Non-polymers , 4 types, 439 molecules

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Myeloperoxidase ... , 3 types, 6 molecules EFACBD

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Sugars , 2 types, 6 molecules

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Non-polymers , 4 types, 439 molecules

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