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Basic information

Entry
Database: PDB / ID: 8ing
TitleStructure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase (LPO) / NO / NO2
Function / homology
Function and homology information


thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress ...thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane / heme binding / calcium ion 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 / NITRIC OXIDE / NITRITE ION / NITRATE ION / 1-(OXIDOSULFANYL)METHANAMINE / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsAhmad, M.I. / Viswanathan, V. / Kumar, M. / Singh, R.P. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)D-560 India
CitationJournal: To be published
Title: Structure of the ternary complex of lactoperoxidase with substrate nitric oxide (NO) and product nitrite ion (NO2) at 1.98 A resolution
Authors: Ahmad, M.I. / Viswanathan, V. / Kumar, M. / Singh, R.P. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionMar 9, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 5, 2023ID: 7WCS
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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)72,13040
Polymers67,6521
Non-polymers4,47839
Water6,593366
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.052, 80.342, 76.121
Angle α, β, γ (deg.)90.000, 102.820, 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


Mass: 67651.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: A0A452E9Y6, 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
#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: obtained synthetically / 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 , 11 types, 401 molecules

#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#7: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#10: 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
#11: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#12: Chemical ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5NOS
#13: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: Sodium nitrate, PEG

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2013
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→35.329 Å / Num. obs: 43516 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 0.96 / Net I/σ(I): 32.4
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 2188 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
AUTOMARdata collection
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→35.329 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.18 / Average fsc free: 0.8986 / Average fsc work: 0.9133 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2335 2188 5.028 %
Rwork0.1829 41328 -
all0.186 --
obs-43516 98.261 %
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: 39.155 Å2
Baniso -1Baniso -2Baniso -3
1-0.012 Å2-0 Å2-0.016 Å2
2--0.013 Å2-0 Å2
3----0.016 Å2
Refinement stepCycle: LAST / Resolution: 1.98→35.329 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4761 0 192 366 5319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135093
X-RAY DIFFRACTIONr_bond_other_d0.0340.0154701
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.6836902
X-RAY DIFFRACTIONr_angle_other_deg2.4321.60610821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41621.756279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54115815
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7231539
X-RAY DIFFRACTIONr_chiral_restr0.0860.2628
X-RAY DIFFRACTIONr_chiral_restr_other2.7710.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025750
X-RAY DIFFRACTIONr_gen_planes_other0.0230.021222
X-RAY DIFFRACTIONr_nbd_refined0.2230.21267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2270.24746
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22407
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2325
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2560.26
X-RAY DIFFRACTIONr_metal_ion_refined0.5680.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.370.233
X-RAY DIFFRACTIONr_nbd_other0.3920.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.26
X-RAY DIFFRACTIONr_mcbond_it4.8383.9942393
X-RAY DIFFRACTIONr_mcbond_other4.843.9912385
X-RAY DIFFRACTIONr_mcangle_it7.3515.9792979
X-RAY DIFFRACTIONr_mcangle_other7.3515.9842979
X-RAY DIFFRACTIONr_scbond_it3.7174.2742700
X-RAY DIFFRACTIONr_scbond_other3.7164.2752701
X-RAY DIFFRACTIONr_scangle_it5.6436.3273921
X-RAY DIFFRACTIONr_scangle_other5.6426.3283922
X-RAY DIFFRACTIONr_lrange_it11.32349.1845994
X-RAY DIFFRACTIONr_lrange_other11.29649.1755986
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
1.98-2.0310.2941500.24727000.2532190.8370.86988.53680.213
2.031-2.0870.3381470.27430100.27731690.8050.82999.62130.242
2.087-2.1470.2661580.21129300.21430980.8940.91299.67720.18
2.147-2.2130.2661400.228410.20329920.8980.91999.63240.173
2.213-2.2850.3711350.35625750.35628930.6820.69593.67440.286
2.285-2.3650.2291430.19727070.19928560.9160.92599.78990.172
2.365-2.4540.2451210.18925840.19227100.9210.92599.81550.172
2.454-2.5530.2161440.15624490.15925950.9440.95499.92290.141
2.553-2.6660.251060.17623790.17924860.9260.94199.95980.163
2.666-2.7960.2421200.17422850.17824050.9270.951000.163
2.796-2.9460.2251300.16921550.17222850.9360.9511000.162
2.946-3.1230.2141100.17520660.17721760.9470.9541000.173
3.123-3.3370.229970.1819540.18320510.9310.9471000.182
3.337-3.6020.2081050.17217300.17418840.950.96497.39920.176
3.602-3.9410.215780.16116320.16417580.9340.95597.26960.171
3.941-4.40.204780.1514500.15215810.9520.96396.64770.169
4.4-5.0670.232750.15613340.1614120.9260.94899.78750.179
5.067-6.1740.233540.16611450.16811990.9440.9531000.189
6.174-8.6010.212560.1748880.1769450.9420.95499.89420.211
8.601-35.3290.202410.1745140.1765630.9540.96498.5790.215

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