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

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Basic information

Entry
Database: PDB / ID: 12cl
TitleCrystal structure of canine myeloperoxidase inhibited by SPIN from Staphylococcus delphini
Components
  • Myeloperoxidase
  • SPIN family peroxidase inhibitor
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / immune evasion / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / Neutrophil degranulation / 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 / nucleosome disassembly ...Events associated with phagocytolytic activity of PMN cells / Neutrophil degranulation / 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 / nucleosome disassembly / azurophil granule / phagocytic vesicle / nucleosome binding / hydrogen peroxide catabolic process / peroxidase activity / heparin binding / response to oxidative stress / defense response to bacterium / heme binding / : / 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. / Haem peroxidase superfamily
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / SPIN family peroxidase inhibitor / Myeloperoxidase
Similarity search - Component
Biological speciesStaphylococcus delphini (bacteria)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFatehi, S. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM140852 United States
CitationJournal: To Be Published
Title: Staphylococcal Peroxidase Inhibitor: Structure/Function Studies on Host-Species Specificity
Authors: Fatehi, S. / Geisbrecht, B.V.
History
DepositionMar 26, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_modification_feature / pdbx_nonpoly_atom_coordination ...pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase
B: Myeloperoxidase
C: SPIN family peroxidase inhibitor
D: SPIN family peroxidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,77338
Polymers184,5974
Non-polymers7,17634
Water15,601866
1
A: Myeloperoxidase
C: SPIN family peroxidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,09821
Polymers92,2982
Non-polymers3,80019
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-85 kcal/mol
Surface area25610 Å2
MethodPISA
2
B: Myeloperoxidase
D: SPIN family peroxidase inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,67517
Polymers92,2982
Non-polymers3,37615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8360 Å2
ΔGint-87 kcal/mol
Surface area25930 Å2
MethodPISA
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 number5
Space group name H-MC121

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Components

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 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-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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
#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
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 , 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 interestN
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: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 9, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 108057 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.06 / Rrim(I) all: 0.158 / Χ2: 0.998 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.1860.905107280.6580.8910.4040.9941.01499.8
2.18-2.266.40.746107770.7690.9320.3210.8141.038100
2.26-2.377.10.618107810.8640.9630.2490.6670.979100
2.37-2.497.10.486107350.9070.9750.1950.5241.003100
2.49-2.657.10.374108220.9390.9840.1510.4041.001100
2.65-2.856.90.272107920.9630.9910.1110.2940.995100
2.85-3.146.40.183107980.9820.9950.0780.1990.983100
3.14-3.596.90.105108100.9940.9990.0430.1131.042100
3.59-4.527.20.065108630.9970.9990.0260.070.965100
4.52-506.80.051109510.9980.9990.0210.0550.963100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.1987 1999 1.86 %
Rwork0.1671 --
obs0.1677 107489 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10256 0 460 866 11582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710943
X-RAY DIFFRACTIONf_angle_d0.94914882
X-RAY DIFFRACTIONf_dihedral_angle_d13.5244196
X-RAY DIFFRACTIONf_chiral_restr0.0491649
X-RAY DIFFRACTIONf_plane_restr0.0091931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26841330.2327016X-RAY DIFFRACTION93
2.15-2.20.21511430.2157516X-RAY DIFFRACTION99
2.2-2.270.23621410.20297475X-RAY DIFFRACTION99
2.27-2.340.25211430.19387567X-RAY DIFFRACTION99
2.34-2.430.20611440.18267535X-RAY DIFFRACTION99
2.43-2.520.23311430.17647542X-RAY DIFFRACTION99
2.52-2.640.2141420.17527524X-RAY DIFFRACTION100
2.64-2.780.2191440.1767563X-RAY DIFFRACTION100
2.78-2.950.23311440.18127578X-RAY DIFFRACTION100
2.95-3.180.22881440.17177610X-RAY DIFFRACTION100
3.18-3.50.18281440.15547600X-RAY DIFFRACTION100
3.5-40.17351440.13987618X-RAY DIFFRACTION100
4.01-5.050.15471450.13637623X-RAY DIFFRACTION100
5.05-49.420.18281450.16987723X-RAY DIFFRACTION100
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)
10.0379-0.0922-0.01320.7542-0.62760.6813-0.04060.1281-0.19890.0185-0.0694-0.2778-0.06980.1147-0.00060.1978-0.0604-0.0020.25350.00110.23985.0659-21.400128.212
20.67940.158-0.22030.68360.36421.1371-0.0750.16630.1076-0.104-0.04710.121-0.2097-0.1715-0.00010.2138-0.0107-0.06090.23670.00970.1839-15.8537-11.588520.5114
31.11090.0857-0.75420.1681-0.0260.4950.01450.37520.2042-0.0490.07750.0464-0.38870.09750.09460.391-0.1421-0.05220.29810.08520.21287.99673.567819.7496
40.93530.4743-0.07420.45360.05770.71160.0276-0.1316-0.01720.0918-0.0205-0.0422-0.18610.10840.10390.2433-0.0884-0.02950.22460.00520.16933.9677-8.944237.1171
50.40240.0996-0.02090.05230.0180.0928-0.07470.18920.8362-0.096-0.00860.2543-0.7676-0.1827-0.0130.61730.0126-0.05650.29340.09930.5323-7.08814.244925.0182
61.08680.682-0.21380.71380.04110.94380.0366-0.06520.10940.0827-0.07350.1336-0.2135-0.18680.0020.21720.0019-0.00860.2185-0.02710.1763-13.7321-10.213734.3195
70.7752-0.17050.00080.5302-0.49560.6371-0.0776-0.39290.52270.36720.08860.0042-0.78050.2717-0.00160.5669-0.158-0.02220.2475-0.09720.39615.951410.347640.4901
80.07490.1554-0.03880.6694-0.05050.501-0.10720.16960.1239-0.08750.05460.12530.0228-0.0676-00.2216-0.0598-0.00170.2711-0.0040.2434-12.3899-37.340826.0992
90.63390.44470.55230.91130.04780.9084-0.18460.3231-0.5378-0.27820.099-0.58220.23910.12750.02020.16360.01980.13510.2087-0.03320.526212.5082-50.314326.9061
100.1164-0.01480.11540.051-0.07710.131-0.16770.2146-0.0661-0.2020.1664-0.13940.0637-0.03260.00010.2392-0.08460.06940.2697-0.03270.2771-5.0487-43.14519.7713
110.39580.1520.26430.2627-0.31280.4510.08590.2793-0.1221-0.2940.0143-0.2390.2629-0.03090.03310.4431-0.12170.12050.2727-0.1160.3679-9.9618-64.709815.5484
120.25080.32610.04750.56580.06510.3523-0.02240.0573-0.2142-0.06290.0878-0.04630.2317-0.15210.14950.3003-0.12430.02110.2876-0.01170.2605-22.6756-59.218527.663
131.14420.67940.30741.0413-0.18540.6154-0.0072-0.0018-0.3524-0.06040.0296-0.43180.17820.0507-0.00230.226-0.01780.04040.18670.00090.38231.2211-56.944833.4121
140.41980.64370.43020.6520.01780.5157-0.0267-0.0312-0.12670.0878-0.0505-0.17680.0335-0.0723-0.03310.1744-0.0436-0.02650.18560.03190.2629-0.6142-45.57542.1434
150.29530.09410.11790.55330.07720.2235-0.0076-0.2624-0.36130.18840.0586-0.07170.3493-0.3355-0.00350.373-0.1187-0.02890.2840.06940.3678-17.8095-67.854739.8901
160.1326-0.08190.01260.0777-0.03520.0064-0.2760.0074-0.5213-0.01680.09-0.0112-0.02070.4029-0.00160.5103-0.2003-0.04770.55550.03690.2612-2.0599-7.820511.8267
170.7012-0.36760.0240.8526-0.27520.1685-0.2010.4321-0.1253-0.00490.46850.0227-0.70080.07770.27630.504-0.30160.00040.5226-0.03040.205320.22161.25088.449
180.01650.0023-0.03810.03590.01390.0432-0.19080.0068-0.18580.26910.4463-0.09670.3564-0.150400.4469-0.1427-0.04320.4626-0.0230.345424.5899-6.465911.4496
190.1445-0.0071-0.0203-0.0097-0.00640.1983-0.12510.620.0778-0.62870.2485-0.0861-0.2429-0.10650.00160.517-0.1983-0.02910.6392-0.00430.260116.56470.1455-0.2242
200.0467-0.0281-0.00550.06510.05680.0322-0.2638-0.09090.36870.08560.2595-0.21950.2372-0.101500.4773-0.16020.16620.4626-0.08050.4519-1.0271-52.083613.4432
210.5753-1.0287-0.00491.8858-0.01730.0272-0.08990.24920.11540.02930.1295-0.40940.4791-0.3985-0.00070.5755-0.29820.10050.5303-0.00830.2156-21.9321-60.72514.1123
220.66860.1458-0.27110.1078-0.14530.26-0.03140.42010.9789-0.11430.3102-0.0514-0.29530.2123-0.02690.5705-0.13230.13770.5930.04780.3754-21.731-54.30031.1288
230.00410.0103-0.00850.0007-0.01130.01590.12730.2163-0.1229-0.2881-0.31760.01160.10940.4784-0.00010.7147-0.04280.13680.6409-0.14060.4451-15.0223-66.2554-2.4217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 167 through 206 )
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 339 )
3X-RAY DIFFRACTION3chain 'A' and (resid 340 through 433 )
4X-RAY DIFFRACTION4chain 'A' and (resid 434 through 504 )
5X-RAY DIFFRACTION5chain 'A' and (resid 505 through 552 )
6X-RAY DIFFRACTION6chain 'A' and (resid 553 through 696 )
7X-RAY DIFFRACTION7chain 'A' and (resid 697 through 743 )
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 206 )
9X-RAY DIFFRACTION9chain 'B' and (resid 207 through 310 )
10X-RAY DIFFRACTION10chain 'B' and (resid 311 through 352 )
11X-RAY DIFFRACTION11chain 'B' and (resid 353 through 409 )
12X-RAY DIFFRACTION12chain 'B' and (resid 410 through 460 )
13X-RAY DIFFRACTION13chain 'B' and (resid 461 through 605 )
14X-RAY DIFFRACTION14chain 'B' and (resid 606 through 696 )
15X-RAY DIFFRACTION15chain 'B' and (resid 697 through 743 )
16X-RAY DIFFRACTION16chain 'C' and (resid 28 through 39 )
17X-RAY DIFFRACTION17chain 'C' and (resid 40 through 60 )
18X-RAY DIFFRACTION18chain 'C' and (resid 61 through 74 )
19X-RAY DIFFRACTION19chain 'C' and (resid 75 through 97 )
20X-RAY DIFFRACTION20chain 'D' and (resid 28 through 39 )
21X-RAY DIFFRACTION21chain 'D' and (resid 40 through 60 )
22X-RAY DIFFRACTION22chain 'D' and (resid 61 through 88 )
23X-RAY DIFFRACTION23chain 'D' and (resid 89 through 97 )

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