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- PDB-7c74: Crystal structure of yak lactoperoxidase using data obtained from... -

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Basic information

Entry
Database: PDB / ID: 7c74
TitleCrystal structure of yak lactoperoxidase using data obtained from crystals soaked in CaCl2 at 2.73 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: 2.73 Å
AuthorsSingh, P.K. / Viswanathan, V. / Pandey, S.N. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, P. / 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 10, 2020ID: 6LO7
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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 1.4Nov 6, 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

Downloads & links

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Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4654
Polymers67,7731
Non-polymers6923
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-30 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.060, 80.590, 74.830
Angle α, β, γ (deg.)90.000, 101.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M CaCl2, 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: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2019 / Details: mirror
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.73→53.01 Å / Num. obs: 16875 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.96 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.079 / Net I/σ(I): 6.5
Reflection shellResolution: 2.73→2.8 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3 / Num. unique obs: 1174 / CC1/2: 0.94 / Rpim(I) all: 0.197 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LO7

6lo7
PDB Unreleased entry


Resolution: 2.73→53.01 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.826 / SU B: 18.094 / SU ML: 0.357 / Cross valid method: FREE R-VALUE / ESU R Free: 0.459
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2919 826 4.907 %
Rwork0.1953 16008 -
all0.2 --
obs-16834 99.704 %
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: 31.186 Å2
Baniso -1Baniso -2Baniso -3
1--0.079 Å2-0 Å20.029 Å2
2---0.216 Å2-0 Å2
3---0.263 Å2
Refinement stepCycle: LAST / Resolution: 2.73→53.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 45 316 5131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134965
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174512
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.6626741
X-RAY DIFFRACTIONr_angle_other_deg1.1641.58310480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5485594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44221.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40115825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.771538
X-RAY DIFFRACTIONr_chiral_restr0.0610.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025560
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021091
X-RAY DIFFRACTIONr_nbd_refined0.2030.21249
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24776
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22286
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1540.211
X-RAY DIFFRACTIONr_nbd_other0.2050.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2380.26
X-RAY DIFFRACTIONr_mcbond_it2.3643.3742382
X-RAY DIFFRACTIONr_mcbond_other2.3463.3722381
X-RAY DIFFRACTIONr_mcangle_it4.0625.0532972
X-RAY DIFFRACTIONr_mcangle_other4.0645.0562973
X-RAY DIFFRACTIONr_scbond_it1.6823.4512583
X-RAY DIFFRACTIONr_scbond_other1.6833.4532581
X-RAY DIFFRACTIONr_scangle_it3.0065.1453769
X-RAY DIFFRACTIONr_scangle_other3.0065.1453769
X-RAY DIFFRACTIONr_lrange_it7.63638.2865835
X-RAY DIFFRACTIONr_lrange_other7.55638.3625789
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
2.73-2.8010.358640.27711740.28112400.8070.81299.83870.256
2.801-2.8770.324550.23511910.2412460.8240.8461000.215
2.877-2.960.358600.23410700.2411300.7740.8591000.216
2.96-3.0510.43470.21111110.21911580.7960.8791000.191
3.051-3.1510.324600.18810340.19510940.8490.8991000.174
3.151-3.2610.327730.2019880.2110610.8550.8921000.19
3.261-3.3840.313490.19310000.19910490.8490.9051000.186
3.384-3.5210.295360.259270.2519770.8840.91298.5670.245
3.521-3.6770.369500.2369080.2449650.8580.88499.27460.235
3.677-3.8560.28400.2178880.229290.8630.88399.89240.22
3.856-4.0630.293410.227840.2238420.8750.91897.9810.221
4.063-4.3080.187370.1457880.1478250.9510.9481000.15
4.308-4.6030.222370.1197550.1247920.950.9641000.122
4.603-4.9690.21290.1387020.1417310.950.9631000.141
4.969-5.4390.279330.1696300.1746630.9320.9521000.174
5.439-6.0720.23300.1795820.1826120.9150.931000.191
6.072-6.9970.33280.1914980.1995260.8770.9181000.203
6.997-8.5320.224280.164360.1644640.9310.9511000.179
8.532-11.9130.189170.1333430.1363610.9660.96799.7230.156
11.913-53.010.327120.2051990.212170.9270.94997.2350.277

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