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- PDB-5mfa: Crystal structure of human promyeloperoxidase (proMPO) -

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Basic information

Entry
Database: PDB / ID: 5mfa
TitleCrystal structure of human promyeloperoxidase (proMPO)
ComponentsMyeloperoxidase
KeywordsOXIDOREDUCTASE / Myeloperoxidase / proMPO / biosynthesis / proteolytic maturation / halide oxidation
Function / homology
Function and homology information


neutrophil-mediated killing of symbiont cell / Events associated with phagocytolytic activity of PMN cells / myeloperoxidase / neutrophil-mediated killing of fungus / neutrophil extracellular trap / neutrophil-mediated killing of bacterium / phagocytic vesicle lumen / response to gold nanoparticle / neutrophil extracellular trap formation / protein-containing complex destabilizing activity ...neutrophil-mediated killing of symbiont cell / Events associated with phagocytolytic activity of PMN cells / myeloperoxidase / neutrophil-mediated killing of fungus / neutrophil extracellular trap / neutrophil-mediated killing of bacterium / phagocytic vesicle lumen / response to gold nanoparticle / neutrophil extracellular trap formation / protein-containing complex destabilizing activity / low-density lipoprotein particle remodeling / nucleosome disassembly / azurophil granule / response to food / response to mechanical stimulus / nucleosome binding / phagocytic vesicle / secretory granule / hydrogen peroxide catabolic process / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to lipopolysaccharide / response to oxidative stress / lysosome / defense response to bacterium / chromatin binding / heme binding / negative regulation of apoptotic process / Neutrophil degranulation / : / extracellular exosome / extracellular region / metal ion binding / nucleus
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / DI(HYDROXYETHYL)ETHER / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGrishkovskaya, I. / Furtmueller, P.G. / Obinger, C. / Djinovic-Carugo, K.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure of human promyeloperoxidase (proMPO) and the role of the propeptide in processing and maturation.
Authors: Grishkovskaya, I. / Paumann-Page, M. / Tscheliessnig, R. / Stampler, J. / Hofbauer, S. / Soudi, M. / Sevcnikar, B. / Oostenbrink, C. / Furtmuller, P.G. / Djinovic-Carugo, K. / Nauseef, W.M. / Obinger, C.
History
DepositionNov 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myeloperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,73619
Polymers79,0481
Non-polymers3,68918
Water13,799766
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-27 kcal/mol
Surface area24170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.152, 109.151, 83.961
Angle α, β, γ (deg.)90.00, 122.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-222-

PHE

21A-932-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myeloperoxidase / MPO


Mass: 79047.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P05164, myeloperoxidase

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Sugars , 3 types, 5 molecules

#2: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 2
Source method: isolated from a genetically manipulated source
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 , 6 types, 779 molecules

#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 10% w/v PEG20000, 20% PEG MME 550, 0.1 mM Tris-Bicine, pH 8.5, 0.05 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.2→44.68 Å / Num. obs: 225738 / % possible obs: 90.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 10.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 1.204 / CC1/2: 0.263 / % possible all: 41.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHL

1mhl


Resolution: 1.2→44.68 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.23
RfactorNum. reflection% reflection
Rfree0.1429 11276 5 %
Rwork0.1233 --
obs0.1243 225654 90.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.2→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 237 766 5697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085383
X-RAY DIFFRACTIONf_angle_d1.1457324
X-RAY DIFFRACTIONf_dihedral_angle_d14.5652140
X-RAY DIFFRACTIONf_chiral_restr0.086791
X-RAY DIFFRACTIONf_plane_restr0.008956
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.21360.31031570.32853181X-RAY DIFFRACTION40
1.2136-1.22790.33791530.30733727X-RAY DIFFRACTION46
1.2279-1.24290.30411840.2944218X-RAY DIFFRACTION53
1.2429-1.25860.28322350.26534735X-RAY DIFFRACTION60
1.2586-1.27520.28152900.24245315X-RAY DIFFRACTION67
1.2752-1.29270.25253340.22995897X-RAY DIFFRACTION74
1.2927-1.31110.2443000.20956553X-RAY DIFFRACTION82
1.3111-1.33070.21163590.18827008X-RAY DIFFRACTION89
1.3307-1.35150.21253960.17437436X-RAY DIFFRACTION94
1.3515-1.37370.18554320.1557761X-RAY DIFFRACTION99
1.3737-1.39730.17454170.14337923X-RAY DIFFRACTION100
1.3973-1.42280.16714060.13377887X-RAY DIFFRACTION100
1.4228-1.45010.15084400.12657903X-RAY DIFFRACTION100
1.4501-1.47970.15424230.11917864X-RAY DIFFRACTION100
1.4797-1.51190.13364580.10967900X-RAY DIFFRACTION100
1.5119-1.54710.13734060.10327914X-RAY DIFFRACTION100
1.5471-1.58580.12434110.0957929X-RAY DIFFRACTION100
1.5858-1.62860.12084260.09527916X-RAY DIFFRACTION100
1.6286-1.67660.11674190.09627869X-RAY DIFFRACTION100
1.6766-1.73070.12374500.09647936X-RAY DIFFRACTION100
1.7307-1.79250.12274010.09897949X-RAY DIFFRACTION100
1.7925-1.86430.12084220.10467908X-RAY DIFFRACTION100
1.8643-1.94920.13353710.10767982X-RAY DIFFRACTION100
1.9492-2.05190.12094070.10827938X-RAY DIFFRACTION100
2.0519-2.18050.12864480.10837886X-RAY DIFFRACTION100
2.1805-2.34880.12414100.10447923X-RAY DIFFRACTION100
2.3488-2.58520.13234130.10977970X-RAY DIFFRACTION100
2.5852-2.95920.14214170.12047954X-RAY DIFFRACTION100
2.9592-3.7280.14514350.12997969X-RAY DIFFRACTION100
3.728-44.71550.13864560.12918027X-RAY DIFFRACTION100

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