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- PDB-7wyj: Structure of the complex of lactoperoxidase with nitric oxide cat... -

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Basic information

Entry
Database: PDB / ID: 7wyj
TitleStructure of the complex of lactoperoxidase with nitric oxide catalytic product nitrite at 1.89 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxide family
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / calcium ion binding ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / calcium ion binding / heme binding / extracellular space / cytoplasm
Similarity search - Function
Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / NITRITE ION / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsViswanathan, V. / Pandey, N. / Singh, A.K. / Sinha, M. / Singh, R.P. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)PDF/2018/000008 India
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Structural evidence of the conversion of nitric oxide (NO) to nitrite ion (NO2-) by lactoperoxidase (LPO): Structure of the complex of LPO with NO2- at 1.89 angstrom resolution
Authors: Viswanathan, V. / Ahmad, M.I. / Singh, P.K. / Ahmad, N. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
SupersessionMar 1, 2023ID: 7VIN
Revision 1.1Mar 1, 2023Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Jul 26, 2023Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)72,78237
Polymers67,7731
Non-polymers5,00836
Water8,665481
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.990, 79.930, 76.310
Angle α, β, γ (deg.)90.000, 102.180, 90.000
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: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#10: 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

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Non-polymers , 8 types, 513 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: Ammonium Iodide, PEG3350, pH6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.89→35.301 Å / Num. obs: 50802 / % possible obs: 99.94 % / Redundancy: 4.3 % / CC1/2: 0.94 / Rsym value: 0.09 / Net I/σ(I): 13.5
Reflection shellResolution: 1.89→1.94 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 3679 / CC1/2: 0.89 / Rsym value: 0.341

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VIN

7vin
PDB Unreleased entry


Resolution: 1.89→35.301 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.211 / SU B: 4.354 / SU ML: 0.129 / Average fsc free: 0.8829 / Average fsc work: 0.9072 / Cross valid method: FREE R-VALUE / ESU R: 0.178 / ESU R Free: 0.167
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.258 2579 5.077 %
Rwork0.2031 48223 -
all0.206 --
obs-50802 99.945 %
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: 34.526 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20 Å20.007 Å2
2---0.013 Å20 Å2
3---0.006 Å2
Refinement stepCycle: LAST / Resolution: 1.89→35.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 161 481 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135067
X-RAY DIFFRACTIONr_bond_other_d0.0030.0154717
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6866888
X-RAY DIFFRACTIONr_angle_other_deg1.3251.60710868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44721.786280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3515829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2521539
X-RAY DIFFRACTIONr_chiral_restr0.0750.2631
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025732
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021227
X-RAY DIFFRACTIONr_nbd_refined0.2460.21267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.24934
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22381
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22200
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2352
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0640.29
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1810.215
X-RAY DIFFRACTIONr_nbd_other0.2630.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2640.216
X-RAY DIFFRACTIONr_mcbond_it3.1583.5022386
X-RAY DIFFRACTIONr_mcbond_other3.1493.4972382
X-RAY DIFFRACTIONr_mcangle_it5.0355.2322978
X-RAY DIFFRACTIONr_mcangle_other5.0355.2372979
X-RAY DIFFRACTIONr_scbond_it2.8323.8162681
X-RAY DIFFRACTIONr_scbond_other2.8323.8172682
X-RAY DIFFRACTIONr_scangle_it4.5985.6353908
X-RAY DIFFRACTIONr_scangle_other4.5975.6363909
X-RAY DIFFRACTIONr_lrange_it8.54541.1836017
X-RAY DIFFRACTIONr_lrange_other8.54441.1836018
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
1.89-1.9390.3191800.26235760.26437570.8380.86599.97340.229
1.939-1.9920.3181780.25734510.2636310.8290.86699.94490.225
1.992-2.0490.2871840.24733610.24935460.8630.87899.97180.22
2.049-2.1120.2972050.24732070.2534120.8380.8771000.226
2.112-2.1810.3271840.23631590.24133440.8530.8999.97010.215
2.181-2.2580.2481630.2230620.22132250.8950.9111000.201
2.258-2.3420.2811460.21529650.21831140.8990.91699.90370.199
2.342-2.4380.2751470.21828500.22129970.8880.9081000.206
2.438-2.5460.2991250.22527680.22928940.880.90299.96540.217
2.546-2.6690.2861410.20725840.2127250.880.9161000.201
2.669-2.8130.3041300.21624980.2226290.8660.91199.9620.217
2.813-2.9820.2681210.20323620.20724840.8920.91699.95970.209
2.982-3.1860.2871310.19622200.20123520.8950.92699.95750.209
3.186-3.4390.2121040.19120730.19221770.9320.9381000.208
3.439-3.7640.229980.17718830.17919820.9310.94799.94950.198
3.764-4.2020.198970.16517560.16618530.9460.9561000.192
4.202-4.8410.199830.1615240.16316070.9530.9581000.191
4.841-5.9010.242780.18412920.18813710.9420.95199.92710.226
5.901-8.2310.255580.20810170.21110750.9370.9421000.248
8.231-35.3010.227260.1816150.1836460.9540.95999.2260.225

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