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- PDB-7c73: Crystal structure of yak lactoperoxidase using data obtained from... -

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Basic information

Entry
Database: PDB / ID: 7c73
TitleCrystal structure of yak lactoperoxidase using data obtained from crystals soaked in MgCl2 at 2.70 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase
Function / homology
Function and homology information


thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane / heme binding / calcium ion binding ...thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane / 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
PROTOPORPHYRIN IX CONTAINING FE / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, P.K. / Pandey, S.N. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / Kaur, 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
DepositionMay 22, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 24, 2020ID: 6LNV
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 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 / _citation_author.name
Revision 1.3Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 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 1.5Oct 30, 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)69,2147
Polymers67,8531
Non-polymers1,3606
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-21 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.880, 79.930, 75.050
Angle α, β, γ (deg.)90.000, 101.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lactoperoxidase


Mass: 67853.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos mutus (wild yak) / References: UniProt: L8ICE9
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M CaCl2, 20% PEG 3350, tris-HCl, pH 8 / PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2019 / Details: MIRROR
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17274 / % possible obs: 98 % / Redundancy: 3.1 % / CC1/2: 0.96 / Rmerge(I) obs: 0.198 / Net I/σ(I): 5
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.96 / Num. unique obs: 1170 / CC1/2: 0.536 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNV

6lnv
PDB Unreleased entry


Resolution: 2.7→47.577 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.819 / WRfactor Rfree: 0.276 / WRfactor Rwork: 0.194 / SU B: 23.703 / SU ML: 0.455 / Average fsc free: 0.8066 / Average fsc work: 0.8408 / Cross valid method: FREE R-VALUE / ESU R Free: 0.479
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3063 843 5.001 %
Rwork0.218 16013 -
all0.222 --
obs-16856 97.58 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.042 Å2-0 Å2-0.071 Å2
2--0.039 Å20 Å2
3---0.029 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 44 242 5103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135011
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174546
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6746805
X-RAY DIFFRACTIONr_angle_other_deg1.2241.59410562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5585594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6821.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.39815824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.21538
X-RAY DIFFRACTIONr_chiral_restr0.0740.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025581
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021097
X-RAY DIFFRACTIONr_nbd_refined0.2480.21354
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.24992
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22325
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22310
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0950.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.20.214
X-RAY DIFFRACTIONr_nbd_other0.2710.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2340.25
X-RAY DIFFRACTIONr_mcbond_it2.0613.8292382
X-RAY DIFFRACTIONr_mcbond_other2.0563.8262381
X-RAY DIFFRACTIONr_mcangle_it3.6445.7372972
X-RAY DIFFRACTIONr_mcangle_other3.6435.742973
X-RAY DIFFRACTIONr_scbond_it1.6763.972629
X-RAY DIFFRACTIONr_scbond_other1.6763.9712630
X-RAY DIFFRACTIONr_scangle_it2.9825.923833
X-RAY DIFFRACTIONr_scangle_other2.9825.9213834
X-RAY DIFFRACTIONr_lrange_it10.50667.86923378
X-RAY DIFFRACTIONr_lrange_other10.49967.9423306
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
2.7-2.770.398540.34411700.34712530.5490.64497.68560.334
2.77-2.8460.417560.32611200.3312350.6130.67495.22270.311
2.846-2.9280.318580.31211140.31311960.7470.69897.99330.292
2.928-3.0180.366600.28610690.2911680.7030.75396.6610.263
3.018-3.1160.333600.24410480.24911350.7930.83897.62110.216
3.116-3.2250.358530.24610190.25110990.7970.84197.54320.22
3.225-3.3460.409390.2479960.25310540.7140.84798.19730.218
3.346-3.4820.384530.2299450.23810180.8270.87198.03540.207
3.482-3.6360.239520.2219040.2229810.8960.8997.45160.201
3.636-3.8120.252470.1818760.1859350.9160.93598.71660.168
3.812-4.0170.238540.1778250.188990.8950.93397.77530.163
4.017-4.2590.323370.1837750.1898260.8670.92398.30510.171
4.259-4.550.261520.1727370.1798030.9140.92498.25650.16
4.55-4.9110.298380.1726830.1797390.8970.93397.56430.16
4.911-5.3740.359310.1646450.1726940.8870.94197.40630.155
5.374-5.9990.262280.1715820.1756210.8880.9498.22870.161
5.999-6.9090.229300.1915120.1945510.9160.91298.36660.179
6.909-8.4170.471140.1694430.1774670.8460.9397.85870.166
8.417-11.7220.232180.1563420.163690.9490.9597.5610.164
11.722-47.5770.17190.2722070.2672270.9410.89795.15420.307

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