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- PDB-3zs0: Human Myeloperoxidase inactivated by TX2 -

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Basic information

Entry
Database: PDB / ID: 3zs0
TitleHuman Myeloperoxidase inactivated by TX2
Components(MYELOPEROXIDASE ...) x 2
KeywordsOXIDOREDUCTASE / ENZYME INACTIVATION / INFLAMMATION / NEUTROPHIL / REACTIVE OXYGEN SPECIES (ROS) / HYPOCHLOROUS ACID
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 lipopolysaccharide / response to oxidative stress / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / heme binding / chromatin binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / metal ion binding
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Chem-ZS0 / Myeloperoxidase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTiden, A.K. / Sjogren, T. / Svensson, M. / Bernlind, A. / Senthilmohan, R. / Auchere, F. / Norman, H. / Markgren, P.O. / Gustavsson, S. / Schmidt, S. ...Tiden, A.K. / Sjogren, T. / Svensson, M. / Bernlind, A. / Senthilmohan, R. / Auchere, F. / Norman, H. / Markgren, P.O. / Gustavsson, S. / Schmidt, S. / Lundquist, S. / Forbes, L.V. / Magon, N.J. / Jameson, G.N. / Eriksson, H. / Kettle, A.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: 2-Thioxanthines are Mechanism-Based Inactivators of Myeloperoxidase that Block Oxidative Stress During Inflammation.
Authors: Tiden, A.K. / Sjogren, T. / Svensson, M. / Bernlind, A. / Senthilmohan, R. / Auchere, F. / Norman, H. / Markgren, P.O. / Gustavsson, S. / Schmidt, S. / Lundquist, S. / Forbes, L.V. / Magon, ...Authors: Tiden, A.K. / Sjogren, T. / Svensson, M. / Bernlind, A. / Senthilmohan, R. / Auchere, F. / Norman, H. / Markgren, P.O. / Gustavsson, S. / Schmidt, S. / Lundquist, S. / Forbes, L.V. / Magon, N.J. / Paton, L.N. / Jameson, G.N. / Eriksson, H. / Kettle, A.J.
History
DepositionJun 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Atomic model / Derived calculations / Other
Revision 1.3Jan 21, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.4Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_validate_chiral / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 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 LIGHT CHAIN
B: MYELOPEROXIDASE LIGHT CHAIN
C: MYELOPEROXIDASE HEAVY CHAIN
D: MYELOPEROXIDASE HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,72227
Polymers131,3064
Non-polymers5,41623
Water10,124562
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33580 Å2
ΔGint-205 kcal/mol
Surface area42700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.905, 64.111, 111.452
Angle α, β, γ (deg.)90.00, 97.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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MYELOPEROXIDASE ... , 2 types, 4 molecules ABCD

#1: Protein MYELOPEROXIDASE LIGHT CHAIN


Mass: 12331.849 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HL-60 / References: UniProt: P05164, myeloperoxidase
#2: Protein MYELOPEROXIDASE HEAVY CHAIN


Mass: 53321.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell line: HL-60 / References: UniProt: P05164, myeloperoxidase

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Sugars , 3 types, 6 molecules

#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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 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-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 4
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 , 7 types, 579 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZS0 / 3-(4-FLUOROBENZYL)-2-THIOXO-1,2,3,7-TETRAHYDRO-6H-PURIN-6-ONE


Mass: 276.289 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H9FN4OS
#7: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 5.5 / Details: pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.085
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Apr 28, 2004 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.085 Å / Relative weight: 1
ReflectionResolution: 2.2→33.63 Å / Num. obs: 62502 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.4 / % possible all: 71.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CXP

1cxp


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.311 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.20682 2875 5.1 %RANDOM
Rwork0.17019 ---
obs0.17203 53998 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.625 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0.43 Å2
2--0.67 Å20 Å2
3----1.89 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9138 0 354 562 10054
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9792.0113304
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.03651136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.95222.918466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.407151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.44515108
X-RAY DIFFRACTIONr_chiral_restr0.110.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0227620
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_it0.5261.55751
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03329300
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.69634026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7614.54004
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 224 -
Rwork0.19 3836 -
obs--94.42 %

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