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- PDB-1myp: X-RAY CRYSTAL STRUCTURE OF CANINE MYELOPEROXIDASE AT 3 ANGSTROMS ... -

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Basic information

Entry
Database: PDB / ID: 1myp
TitleX-RAY CRYSTAL STRUCTURE OF CANINE MYELOPEROXIDASE AT 3 ANGSTROMS RESOLUTION
Components(MYELOPEROXIDASE) x 2
KeywordsMYELOPEROXIDASE
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 / response to food / azurophil granule ...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 / response to food / azurophil granule / defense response to fungus / response to mechanical stimulus / removal of superoxide radicals / hydrogen peroxide catabolic process / secretory granule / peroxidase activity / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / heme binding / Neutrophil degranulation / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / 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 / Myeloperoxidase
Similarity search - Component
Biological speciesCanis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsFenna, R.E. / Zeng, J.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: X-ray crystal structure of canine myeloperoxidase at 3 A resolution.
Authors: Zeng, J. / Fenna, R.E.
History
DepositionApr 15, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.process_site / _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_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 / _pdbx_validate_close_contact.auth_asym_id_2 / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYELOPEROXIDASE
C: MYELOPEROXIDASE
B: MYELOPEROXIDASE
D: MYELOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,96014
Polymers131,1004
Non-polymers3,86010
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30710 Å2
ΔGint-147 kcal/mol
Surface area41110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.000, 133.000, 203.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Atom site foot note1: PHE C 203 - GLN C 204 OMEGA =211.23 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: TYR C 557 - PRO C 558 OMEGA =132.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: PRO D 355 - ASN D 356 OMEGA =146.58 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: PRO D 558 - ARG D 559 OMEGA =219.17 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein MYELOPEROXIDASE /


Mass: 12331.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / References: UniProt: P05164, peroxidase
#2: Protein MYELOPEROXIDASE /


Mass: 53218.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / References: UniProt: P05164, peroxidase
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Mass: 424.401 Da / Num. of mol.: 6
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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
Compound detailsEACH HALF-MOLECULE HAS 2 POLYPEPTIDE CHAINS RESULTING FROM POST-TRANSLATIONAL EXCISION OF RESIDUES 107 TO 112.
Nonpolymer detailsTHE EXACT CHEMICAL STRUCTURE OF THE HEME IN MYELOPEROXIDASE IS NOT KNOWN. THE AUTHORS HAVE USED ...THE EXACT CHEMICAL STRUCTURE OF THE HEME IN MYELOPEROXIDASE IS NOT KNOWN. THE AUTHORS HAVE USED PROTOPORPHYRIN IX AS A MODEL. A HEME IS COVALENTLY BOUND TO THE LARGE POLYPEPTIDE IN EACH HALF OF THE MOLECULE, BUT THE CHEMICAL NATURE OF THE LINK IS NOT KNOWN. THE LINK APPEARS TO INVOLVE THE CARBOXYLATE GROUP OF GLU 242. EACH HALF-MOLECULE INCLUDES A BOUND CALCIUM ION WITH POSSIBLE LIGANDS INCLUDING: ASP 96 CARBOXYLATE OXYGEN, ASP 96 PEPTIDE CARBONYL OXYGEN, THR 168 HYDROXYL OXYGEN, PHE 170 PEPTIDE CARBONYL OXYGEN, ASP 172 CARBOXYLATE OXYGEN, AND SER 174 HYDROXYL OXYGEN.
Sequence detailsTHE SEQUENCE FOR HUMAN MYELOPEROXIDASE HAS BEEN USED TO INTERPRET THE ELECTRON DENSITY MAP OF DOG ...THE SEQUENCE FOR HUMAN MYELOPEROXIDASE HAS BEEN USED TO INTERPRET THE ELECTRON DENSITY MAP OF DOG MYELOPEROXIDASE. THE SEQUENCE NUMBERING BEGINNING WITH CYS 1 WAS CHOSEN TO FACILITATE COMPARISONS BETWEEN OTHER MEMBERS OF THE GENE FAMILY INCLUDING LACTOPEROXIDASE, EOSINOPHIL PEROXIDASE AND THYROID PEROXIDASE. AMINO-TERMINAL SEQUENCING HAS INDICATED 2 RESIDUES PRIOR TO THIS CYSTEINE (VAL, THR) IN HUMAN MYELOPEROXIDASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal grow
*PLUS
Temperature: 15-20 ℃ / Method: vapor diffusion, hanging drop / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mg/mlprotein1drop
21.3 Mammonium phosphate1drop
350 mMPIPES1drop
41.7-1.8 Mammonium sulfate1reservoir
51.3 Mammonium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.1 Å / Num. obs: 33190 / % possible obs: 97 % / Num. measured all: 214889 / Rmerge(I) obs: 0.0773

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.257 / Highest resolution: 3 Å
Details: THE HUMAN MYELOPEROXIDASE SEQUENCE INCLUDES 4 POTENTIAL SITES FOR ASPARAGINE-LINKED GLYCOSYLATION IN EACH HALF OF THE MOLECULE AT POSITIONS: ASN 157, ASN 189, ASN 225, ASN 317. THE AUTHORS ...Details: THE HUMAN MYELOPEROXIDASE SEQUENCE INCLUDES 4 POTENTIAL SITES FOR ASPARAGINE-LINKED GLYCOSYLATION IN EACH HALF OF THE MOLECULE AT POSITIONS: ASN 157, ASN 189, ASN 225, ASN 317. THE AUTHORS DO NOT SEE CLEAR EVIDENCE FOR GLYCOSYLATION AT ASN 157 IN DOG MYELOPEROXIDASE. AT EACH OF THE OTHER 3 SITES TWO N-ACETYLGLUCOSAMINES ARE SEEN AND HAVE BEEN INCLUDED IN THE MODEL. ASN 317 OCCURS AT THE DIMER INTERFACE AND DENSITY CORRESPONDING TO 3 ADDITIONAL MANNOSE SUGARS AND A FUCOSE CAN BE SEEN. THESE SUGARS HAVE NOT BEEN INCLUDED IN THE MODEL BECAUSE THEIR PRECISE ORIENTATIONS CANNOT BE DETERMINED AT PRESENT.
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8878 0 256 0 9134
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg3.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. reflection obs: 32064 / Rfactor obs: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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