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- PDB-6l5g: Crystal structure of yak lactoperoxidase with disordered heme moi... -

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Basic information

Entry
Database: PDB / ID: 6l5g
TitleCrystal structure of yak lactoperoxidase with disordered heme moiety at 2.50 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / defense response to bacterium / calcium ion binding / heme binding / extracellular space / metal ion binding / 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
PROTOPORPHYRIN IX CONTAINING FE / : / Lactoperoxidase / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSingh, P.K. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2021
Title: Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution.
Authors: Singh, P.K. / Pandey, S. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_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_label_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_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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 3, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,12215
Polymers67,7731
Non-polymers2,34914
Water6,377354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-13 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.820, 84.710, 99.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lactoperoxidase


Mass: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos mutus (wild yak) / References: UniProt: L8ICE9, UniProt: P80025*PLUS

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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
#3: 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 / Feature type: SUBJECT OF INVESTIGATION
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, 364 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 50.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Potassium fluoride, 20% PEG 3350 / PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2019 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→64.38 Å / Num. obs: 23901 / % possible obs: 100 % / Redundancy: 11.6 % / CC1/2: 0.99 / Rsym value: 0.2 / Net I/σ(I): 7.5
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2648 / CC1/2: 0.818 / Rsym value: 0.845 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3bxi

3bxi


Resolution: 2.5→64.375 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.441 / SU ML: 0.237 / Cross valid method: FREE R-VALUE / ESU R: 0.86 / ESU R Free: 0.294
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2394 1136 4.77 %
Rwork0.1846 --
all0.187 --
obs-23818 99.866 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.275 Å2
Baniso -1Baniso -2Baniso -3
1--2.347 Å20 Å20 Å2
2---1.193 Å20 Å2
3---3.54 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 147 354 5271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174598
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6876897
X-RAY DIFFRACTIONr_angle_other_deg1.2291.60210693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5445594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69321.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62415825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5661538
X-RAY DIFFRACTIONr_chiral_restr0.0680.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025641
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021105
X-RAY DIFFRACTIONr_nbd_refined0.2380.21217
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.24693
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22379
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.22
X-RAY DIFFRACTIONr_metal_ion_refined0.3120.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3210.218
X-RAY DIFFRACTIONr_nbd_other0.290.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5510.210
X-RAY DIFFRACTIONr_mcbond_it2.8993.4822379
X-RAY DIFFRACTIONr_mcbond_other2.8533.4792378
X-RAY DIFFRACTIONr_mcangle_it4.875.2112972
X-RAY DIFFRACTIONr_mcangle_other4.8765.2162973
X-RAY DIFFRACTIONr_scbond_it2.8463.6872686
X-RAY DIFFRACTIONr_scbond_other2.8463.6872687
X-RAY DIFFRACTIONr_scangle_it4.8095.4353923
X-RAY DIFFRACTIONr_scangle_other4.8085.4363924
X-RAY DIFFRACTIONr_lrange_it8.93661.75621906
X-RAY DIFFRACTIONr_lrange_other8.93561.75621907
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.5-2.5650.313790.25316310.25517120.7370.899.88320.226
2.565-2.6350.293620.23316280.23516910.8230.84199.94090.207
2.635-2.7110.405690.30315690.30716430.670.73299.69570.279
2.711-2.7950.272670.2515120.25115810.790.80799.87350.223
2.795-2.8860.317670.20714990.21115680.8620.8999.87240.184
2.886-2.9870.324640.18914390.19515040.8620.91499.93350.166
2.987-3.10.285770.18313870.18914640.8960.9231000.162
3.1-3.2260.256720.17613120.1813840.9080.9371000.157
3.226-3.3690.218660.16812930.1713600.9360.94699.92650.153
3.369-3.5330.201580.18512370.18612990.9440.94699.69210.171
3.533-3.7230.232550.17211510.17512090.9310.95399.75190.162
3.723-3.9480.208600.16911120.17111770.9440.95599.57520.161
3.948-4.220.18550.1410440.14210990.9620.9711000.137
4.22-4.5560.179480.1339790.13510270.9680.9731000.134
4.556-4.9890.21550.1389080.1429630.960.9721000.14
4.989-5.5730.208600.1568040.1598640.960.9641000.157
5.573-6.4280.249300.1917400.1947710.9440.95699.87030.19
6.428-7.8530.216390.1786330.1816720.9580.9641000.184
7.853-11.0240.234350.1615000.1655350.9590.9691000.175
11.024-64.3750.211180.2713040.2683260.9620.93298.7730.296

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