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- PDB-1cxp: CRYOGENIC CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C -

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Entry
Database: PDB / ID: 1cxp
TitleCRYOGENIC CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C
Components(MYELOPEROXIDASE) x 2
KeywordsOXIDOREDUCTASE / HEME-PROTEIN / PEROXIDASE
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / myeloperoxidase / response to gold nanoparticle / hypochlorous acid biosynthetic process / phagocytic vesicle lumen / respiratory burst involved in defense response / response to food / low-density lipoprotein particle remodeling / azurophil granule / response to yeast ...Events associated with phagocytolytic activity of PMN cells / myeloperoxidase / response to gold nanoparticle / hypochlorous acid biosynthetic process / phagocytic vesicle lumen / respiratory burst involved in defense response / response to food / low-density lipoprotein particle remodeling / azurophil granule / response to yeast / removal of superoxide radicals / defense response to fungus / response to mechanical stimulus / secretory granule / peroxidase activity / hydrogen peroxide catabolic process / defense response / azurophil granule lumen / heparin binding / response to oxidative stress / response to lipopolysaccharide / lysosome / aging / defense response to bacterium / intracellular membrane-bounded organelle / chromatin binding / Neutrophil degranulation / heme binding / negative regulation of apoptotic process / extracellular space / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Myeloperoxidase / Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Animal heme peroxidase superfamily profile. / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Myeloperoxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsFiedler, T.J. / Fenna, R.E.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: X-ray crystal structure and characterization of halide-binding sites of human myeloperoxidase at 1.8 A resolution.
Authors: Fiedler, T.J. / Davey, C.A. / Fenna, R.E.
#1: Journal: Arch.Biochem.Biophys. / Year: 1995
Title: Structure of the Green Heme in Myeloperoxidase
Authors: Fenna, R. / Zeng, J. / Davey, C.
#2: Journal: Biochemistry / Year: 1996
Title: 2.3 Angstrom Resolution X-Ray Crystal Structure of the Bisubstrate Analogue Inhibitor Salicylhydroxamic Acid Bound to Human Myeloperoxidase: A Model for a Prereaction Complex with Hydrogen Peroxide
Authors: Davey, C.A. / Fenna, R.E.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: X-Ray Crystal Structure of Canine Myeloperoxidase at 3 Angstrom Resolution
Authors: Zeng, J. / Fenna, R.E.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1994
Title: Site-Directed Mutagenesis of Human Myeloperoxidase: Further Identification of Residues Involved in Catalytic Activity and Heme Interaction
Authors: Jacquet, A. / Garcia-Quintana, L. / Deleersnyder, V. / Fenna, R. / Bollen, A. / Moguilevsky, N.
History
DepositionAug 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _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_PDB_ins_code / _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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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_ref_seq_dif.details
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)135,30025
Polymers130,2754
Non-polymers5,02521
Water15,097838
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: MYELOPEROXIDASE
C: MYELOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,69813
Polymers65,1382
Non-polymers2,56111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15250 Å2
ΔGint-95 kcal/mol
Surface area22990 Å2
MethodPISA
3
B: MYELOPEROXIDASE
D: MYELOPEROXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,60212
Polymers65,1382
Non-polymers2,46510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-85 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)111.030, 63.380, 92.170
Angle α, β, γ (deg.)90.00, 97.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.60975, 0.67889, -0.40903), (0.68132, 0.18528, -0.70815), (-0.40497, -0.71048, -0.57552)
Vector: 48.06874, -6.94558, 34.28273)

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein MYELOPEROXIDASE /


Mass: 11903.343 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: NEUTROPHIL / Tissue: BLOOD / References: UniProt: P05164, peroxidase
#2: Protein MYELOPEROXIDASE /


Mass: 53234.191 Da / Num. of mol.: 2 / Fragment: HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: NEUTROPHIL / Tissue: BLOOD / References: UniProt: P05164, peroxidase

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Sugars , 2 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.: 2
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)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


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 , 6 types, 853 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 838 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: POLYETHYLENE GLYCOL 8000, AMMONIUM SULFATE, SODIUM ACETATE, CALCIUM CHLORIDE, pH 5.50, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlMPO1drop
250 mMsodium acetate1drop
350 mMammonium sulfate1drop
42 mM1dropCaCl2
56 %(w/v)PEG80001drop
622-25 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 13, 1997 / Details: LONG FOCUSING MIRRORS, ADSC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 128125 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 16.82 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.6
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.92 / % possible all: 99.4
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 50 Å / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Num. measured all: 525526
Reflection shell
*PLUS
% possible obs: 99.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 5.92

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 1.8→30 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.239 5714 5 %
Rwork0.197 --
obs0.197 113220 96.1 %
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9142 0 327 838 10307
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: MATRIX 1 RELATES CHAIN A TO CHAIN B
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.292 512 5 %
Rwork0.266 9904 -
obs--88.65 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.292 / Rfactor Rwork: 0.266 / Rfactor obs: 0.266

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