PDB-12cl: Crystal structure of canine myeloperoxidase inhibited by SPIN fro...

ID or keywords:

Entry

Database: PDB / ID: 12cl

Title

Crystal structure of canine myeloperoxidase inhibited by SPIN from Staphylococcus delphini

Components

Myeloperoxidase
SPIN family peroxidase inhibitor

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / immune evasion / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

Neutrophil degranulation / Events associated with phagocytolytic activity of PMN cells / myeloperoxidase / neutrophil extracellular trap / neutrophil-mediated killing of bacterium / neutrophil extracellular trap formation / neutrophil-mediated killing of fungus / protein-containing complex destabilizing activity / low-density lipoprotein particle remodeling / azurophil granule ...
Similarity search - Function

Biological species

Staphylococcus delphini (bacteria)

Canis lupus familiaris (dog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Fatehi, S. / Geisbrecht, B.V.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Staphylococcal Peroxidase Inhibitor: Structure/Function Studies on Host-Species Specificity
Authors: Fatehi, S. / Geisbrecht, B.V.

History

Deposition	Mar 26, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	12cl.cif.gz	560.4 KB	Display	PDBx/mmCIF format
PDB format	pdb12cl.ent.gz	455.6 KB	Display	PDB format
PDBx/mmJSON format	12cl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2c/12cl ftp://data.pdbj.org/pub/pdb/validation_reports/2c/12cl	HTTPS FTP

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Related structure data

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

A: Myeloperoxidase

B: Myeloperoxidase

C: SPIN family peroxidase inhibitor

D: SPIN family peroxidase inhibitor

hetero molecules

192 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Myeloperoxidase

C: SPIN family peroxidase inhibitor

hetero molecules

defined by author&software
Evidence: gel filtration
96.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Myeloperoxidase

D: SPIN family peroxidase inhibitor

hetero molecules

defined by author&software
95.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.697, 145.377, 107.610
Angle α, β, γ (deg.)	90.00, 114.85, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 2 types, 4 molecules ABCD

#1: Protein	Myeloperoxidase Mass: 83686.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog) / Tissue: Neutrophil / References: UniProt: A0A8I3P7A7, myeloperoxidase
#2: Protein	SPIN family peroxidase inhibitor Mass: 8611.450 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus delphini (bacteria) / Gene: B5C08_06775 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A4GXB5

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Sugars , 3 types, 7 molecules

#3: Polysaccharide

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

Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}	LINUCS	PDB-CARE

#4: Polysaccharide

alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...

Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 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-e1	WURCS	PDB2Glycan 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]{}}	LINUCS	PDB-CARE

#8: 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.: 3 / 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 , 7 types, 893 molecules

#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: Ca
#6: Chemical	ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₄H₃₂FeN₄O₄
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#10: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#11: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO₄
#12: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 866 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
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: 2.55 Å³/Da / Density % sol: 51.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M acetate (pH 4.3) 1.8 M ammonium sulfate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 9, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 2.09→50 Å / Num. obs: 108057 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.145 / R_pim(I) all: 0.06 / R_rim(I) all: 0.158 / Χ²: 0.998 / Net I/σ(I): 6.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.1-2.18	6	0.905	10728	0.658	0.891	0.404	0.994	1.014	99.8
2.18-2.26	6.4	0.746	10777	0.769	0.932	0.321	0.814	1.038	100
2.26-2.37	7.1	0.618	10781	0.864	0.963	0.249	0.667	0.979	100
2.37-2.49	7.1	0.486	10735	0.907	0.975	0.195	0.524	1.003	100
2.49-2.65	7.1	0.374	10822	0.939	0.984	0.151	0.404	1.001	100
2.65-2.85	6.9	0.272	10792	0.963	0.991	0.111	0.294	0.995	100
2.85-3.14	6.4	0.183	10798	0.982	0.995	0.078	0.199	0.983	100
3.14-3.59	6.9	0.105	10810	0.994	0.999	0.043	0.113	1.042	100
3.59-4.52	7.2	0.065	10863	0.997	0.999	0.026	0.07	0.965	100
4.52-50	6.8	0.051	10951	0.998	0.999	0.021	0.055	0.963	100

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→49.42 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1987	1999	1.86 %
R_work	0.1671	-	-
obs	0.1677	107489	99.03 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.1→49.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10256	0	460	866	11582

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10943
X-RAY DIFFRACTION	f_angle_d	0.949	14882
X-RAY DIFFRACTION	f_dihedral_angle_d	13.524	4196
X-RAY DIFFRACTION	f_chiral_restr	0.049	1649
X-RAY DIFFRACTION	f_plane_restr	0.009	1931

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 (%)
2.1-2.15	0.2684	133	0.232	7016	X-RAY DIFFRACTION	93
2.15-2.2	0.2151	143	0.215	7516	X-RAY DIFFRACTION	99
2.2-2.27	0.2362	141	0.2029	7475	X-RAY DIFFRACTION	99
2.27-2.34	0.2521	143	0.1938	7567	X-RAY DIFFRACTION	99
2.34-2.43	0.2061	144	0.1826	7535	X-RAY DIFFRACTION	99
2.43-2.52	0.2331	143	0.1764	7542	X-RAY DIFFRACTION	99
2.52-2.64	0.214	142	0.1752	7524	X-RAY DIFFRACTION	100
2.64-2.78	0.219	144	0.176	7563	X-RAY DIFFRACTION	100
2.78-2.95	0.2331	144	0.1812	7578	X-RAY DIFFRACTION	100
2.95-3.18	0.2288	144	0.1717	7610	X-RAY DIFFRACTION	100
3.18-3.5	0.1828	144	0.1554	7600	X-RAY DIFFRACTION	100
3.5-4	0.1735	144	0.1398	7618	X-RAY DIFFRACTION	100
4.01-5.05	0.1547	145	0.1363	7623	X-RAY DIFFRACTION	100
5.05-49.42	0.1828	145	0.1698	7723	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	0.0379	-0.0922	-0.0132	0.7542	-0.6276	0.6813	-0.0406	0.1281	-0.1989	0.0185	-0.0694	-0.2778	-0.0698	0.1147	-0.0006	0.1978	-0.0604	-0.002	0.2535	0.0011	0.2398	5.0659	-21.4001	28.212
2	0.6794	0.158	-0.2203	0.6836	0.3642	1.1371	-0.075	0.1663	0.1076	-0.104	-0.0471	0.121	-0.2097	-0.1715	-0.0001	0.2138	-0.0107	-0.0609	0.2367	0.0097	0.1839	-15.8537	-11.5885	20.5114
3	1.1109	0.0857	-0.7542	0.1681	-0.026	0.495	0.0145	0.3752	0.2042	-0.049	0.0775	0.0464	-0.3887	0.0975	0.0946	0.391	-0.1421	-0.0522	0.2981	0.0852	0.2128	7.9967	3.5678	19.7496
4	0.9353	0.4743	-0.0742	0.4536	0.0577	0.7116	0.0276	-0.1316	-0.0172	0.0918	-0.0205	-0.0422	-0.1861	0.1084	0.1039	0.2433	-0.0884	-0.0295	0.2246	0.0052	0.1693	3.9677	-8.9442	37.1171
5	0.4024	0.0996	-0.0209	0.0523	0.018	0.0928	-0.0747	0.1892	0.8362	-0.096	-0.0086	0.2543	-0.7676	-0.1827	-0.013	0.6173	0.0126	-0.0565	0.2934	0.0993	0.5323	-7.088	14.2449	25.0182
6	1.0868	0.682	-0.2138	0.7138	0.0411	0.9438	0.0366	-0.0652	0.1094	0.0827	-0.0735	0.1336	-0.2135	-0.1868	0.002	0.2172	0.0019	-0.0086	0.2185	-0.0271	0.1763	-13.7321	-10.2137	34.3195
7	0.7752	-0.1705	0.0008	0.5302	-0.4956	0.6371	-0.0776	-0.3929	0.5227	0.3672	0.0886	0.0042	-0.7805	0.2717	-0.0016	0.5669	-0.158	-0.0222	0.2475	-0.0972	0.3961	5.9514	10.3476	40.4901
8	0.0749	0.1554	-0.0388	0.6694	-0.0505	0.501	-0.1072	0.1696	0.1239	-0.0875	0.0546	0.1253	0.0228	-0.0676	-0	0.2216	-0.0598	-0.0017	0.2711	-0.004	0.2434	-12.3899	-37.3408	26.0992
9	0.6339	0.4447	0.5523	0.9113	0.0478	0.9084	-0.1846	0.3231	-0.5378	-0.2782	0.099	-0.5822	0.2391	0.1275	0.0202	0.1636	0.0198	0.1351	0.2087	-0.0332	0.5262	12.5082	-50.3143	26.9061
10	0.1164	-0.0148	0.1154	0.051	-0.0771	0.131	-0.1677	0.2146	-0.0661	-0.202	0.1664	-0.1394	0.0637	-0.0326	0.0001	0.2392	-0.0846	0.0694	0.2697	-0.0327	0.2771	-5.0487	-43.145	19.7713
11	0.3958	0.152	0.2643	0.2627	-0.3128	0.451	0.0859	0.2793	-0.1221	-0.294	0.0143	-0.239	0.2629	-0.0309	0.0331	0.4431	-0.1217	0.1205	0.2727	-0.116	0.3679	-9.9618	-64.7098	15.5484
12	0.2508	0.3261	0.0475	0.5658	0.0651	0.3523	-0.0224	0.0573	-0.2142	-0.0629	0.0878	-0.0463	0.2317	-0.1521	0.1495	0.3003	-0.1243	0.0211	0.2876	-0.0117	0.2605	-22.6756	-59.2185	27.663
13	1.1442	0.6794	0.3074	1.0413	-0.1854	0.6154	-0.0072	-0.0018	-0.3524	-0.0604	0.0296	-0.4318	0.1782	0.0507	-0.0023	0.226	-0.0178	0.0404	0.1867	0.0009	0.3823	1.2211	-56.9448	33.4121
14	0.4198	0.6437	0.4302	0.652	0.0178	0.5157	-0.0267	-0.0312	-0.1267	0.0878	-0.0505	-0.1768	0.0335	-0.0723	-0.0331	0.1744	-0.0436	-0.0265	0.1856	0.0319	0.2629	-0.6142	-45.575	42.1434
15	0.2953	0.0941	0.1179	0.5533	0.0772	0.2235	-0.0076	-0.2624	-0.3613	0.1884	0.0586	-0.0717	0.3493	-0.3355	-0.0035	0.373	-0.1187	-0.0289	0.284	0.0694	0.3678	-17.8095	-67.8547	39.8901
16	0.1326	-0.0819	0.0126	0.0777	-0.0352	0.0064	-0.276	0.0074	-0.5213	-0.0168	0.09	-0.0112	-0.0207	0.4029	-0.0016	0.5103	-0.2003	-0.0477	0.5555	0.0369	0.2612	-2.0599	-7.8205	11.8267
17	0.7012	-0.3676	0.024	0.8526	-0.2752	0.1685	-0.201	0.4321	-0.1253	-0.0049	0.4685	0.0227	-0.7008	0.0777	0.2763	0.504	-0.3016	0.0004	0.5226	-0.0304	0.2053	20.2216	1.2508	8.449
18	0.0165	0.0023	-0.0381	0.0359	0.0139	0.0432	-0.1908	0.0068	-0.1858	0.2691	0.4463	-0.0967	0.3564	-0.1504	0	0.4469	-0.1427	-0.0432	0.4626	-0.023	0.3454	24.5899	-6.4659	11.4496
19	0.1445	-0.0071	-0.0203	-0.0097	-0.0064	0.1983	-0.1251	0.62	0.0778	-0.6287	0.2485	-0.0861	-0.2429	-0.1065	0.0016	0.517	-0.1983	-0.0291	0.6392	-0.0043	0.2601	16.5647	0.1455	-0.2242
20	0.0467	-0.0281	-0.0055	0.0651	0.0568	0.0322	-0.2638	-0.0909	0.3687	0.0856	0.2595	-0.2195	0.2372	-0.1015	0	0.4773	-0.1602	0.1662	0.4626	-0.0805	0.4519	-1.0271	-52.0836	13.4432
21	0.5753	-1.0287	-0.0049	1.8858	-0.0173	0.0272	-0.0899	0.2492	0.1154	0.0293	0.1295	-0.4094	0.4791	-0.3985	-0.0007	0.5755	-0.2982	0.1005	0.5303	-0.0083	0.2156	-21.9321	-60.7251	4.1123
22	0.6686	0.1458	-0.2711	0.1078	-0.1453	0.26	-0.0314	0.4201	0.9789	-0.1143	0.3102	-0.0514	-0.2953	0.2123	-0.0269	0.5705	-0.1323	0.1377	0.593	0.0478	0.3754	-21.731	-54.3003	1.1288
23	0.0041	0.0103	-0.0085	0.0007	-0.0113	0.0159	0.1273	0.2163	-0.1229	-0.2881	-0.3176	0.0116	0.1094	0.4784	-0.0001	0.7147	-0.0428	0.1368	0.6409	-0.1406	0.4451	-15.0223	-66.2554	-2.4217

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 167 through 206 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 207 through 339 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 340 through 433 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 434 through 504 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 505 through 552 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 553 through 696 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 697 through 743 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 167 through 206 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 207 through 310 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 311 through 352 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 353 through 409 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 410 through 460 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 461 through 605 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 606 through 696 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 697 through 743 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 28 through 39 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 40 through 60 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 61 through 74 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 75 through 97 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 28 through 39 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 40 through 60 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 61 through 88 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 89 through 97 )

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