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- PDB-5wv3: Crystal structure of bovine lactoperoxidase with a partial Glu258... -

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Basic information

Entry
Database: PDB / ID: 5wv3
TitleCrystal structure of bovine lactoperoxidase with a partial Glu258-heme linkage at 2.07 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / heme binding ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / heme binding / calcium ion binding / extracellular space / cytoplasm
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. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / 1-(OXIDOSULFANYL)METHANAMINE / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsSingh, P.K. / Sirohi, H.V. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Prog. Biophys. Mol. Biol. / Year: 2018
Title: Structural basis of activation of mammalian heme peroxidases
Authors: Singh, P.K. / Iqbal, N. / Sirohi, H.V. / Bairagya, H.R. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 21, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
SupersessionMar 8, 2017ID: 5K1E
Revision 1.1Mar 8, 2017Group: Other
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.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.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: 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 3.0Mar 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_database_related / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
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_seq_id / _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_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,02023
Polymers67,8391
Non-polymers3,18122
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-7 kcal/mol
Surface area24520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.012, 79.809, 66.106
Angle α, β, γ (deg.)90.00, 93.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lactoperoxidase / LPO


Mass: 67839.344 Da / Num. of mol.: 1 / Fragment: UNP residues 118-712 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P80025, peroxidase

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Sugars , 2 types, 4 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.: 1
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
#5: 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: 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, 287 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: CH5NOS
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#9: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Br
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaNO3, PEG3350, pH6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 26, 2015 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.07→66.01 Å / Num. obs: 32253 / % possible obs: 94.6 % / Redundancy: 4.2 % / Rsym value: 0.07 / Net I/σ(I): 17.3
Reflection shellResolution: 2.07→2.11 Å / Mean I/σ(I) obs: 2.3 / % possible all: 69.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K1E

5k1e
PDB Unreleased entry


Resolution: 2.07→34.17 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.464 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.253 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23601 1001 3.1 %RANDOM
Rwork0.16711 ---
obs0.16918 31234 94.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.971 Å2
Baniso -1Baniso -2Baniso -3
1--2.21 Å20 Å2-1.05 Å2
2---2.33 Å20 Å2
3---4.63 Å2
Refinement stepCycle: 1 / Resolution: 2.07→34.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 170 269 5210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195083
X-RAY DIFFRACTIONr_bond_other_d0.0020.024638
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.9886882
X-RAY DIFFRACTIONr_angle_other_deg1.261310765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.295594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33723.739238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86415831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4111538
X-RAY DIFFRACTIONr_chiral_restr0.1410.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215568
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021074
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_it2.0723.1592392
X-RAY DIFFRACTIONr_mcbond_other2.0733.1582381
X-RAY DIFFRACTIONr_mcangle_it3.3984.7292982
X-RAY DIFFRACTIONr_mcangle_other3.3934.7322973
X-RAY DIFFRACTIONr_scbond_it2.0013.362691
X-RAY DIFFRACTIONr_scbond_other1.9983.362691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1084.9853901
X-RAY DIFFRACTIONr_long_range_B_refined8.40259.32624641
X-RAY DIFFRACTIONr_long_range_B_other8.40259.32424641
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.072→2.126 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 55 -
Rwork0.25 1664 -
obs--69.26 %
Refinement TLS params.Method: refined / Origin x: 13.9999 Å / Origin y: -0.4154 Å / Origin z: 18.2943 Å
111213212223313233
T0.0208 Å20.0029 Å2-0.0232 Å2-0.099 Å20.0114 Å2--0.0347 Å2
L2.2963 °20.3606 °20.5999 °2-3.0608 °20.0274 °2--1.5799 °2
S-0.0945 Å °0.2677 Å °0.084 Å °-0.2059 Å °0.0736 Å °0.3211 Å °-0.099 Å °-0.2351 Å °0.0209 Å °

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