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- PDB-9m0i: Structure of the intermediate of lactoperoxidase formed with thio... -

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Basic information

Entry
Database: PDB / ID: 9m0i
TitleStructure of the intermediate of lactoperoxidase formed with thiocynate and hydrogen peroxidase at 1.99 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase (LPO) / Peroxide family
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / heme binding ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / 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 / HYDROGEN PEROXIDE / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsViswanathan, V. / Maurya, A. / Sirohi, H.V. / Kushwaha, G.S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchIR-661 India
CitationJournal: To Be Published
Title: Structure of the intermediate of lactoperoxidase formed with thiocynate and hydrogen peroxidase at 1.99 A resolution.
Authors: Viswanathan, V. / Maurya, A. / Sirohi, H.V. / Kushwaha, G.S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBJ
SupersessionMar 26, 2025ID: 6LCO
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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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)72,42735
Polymers67,7731
Non-polymers4,65434
Water7,152397
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.270, 80.441, 76.599
Angle α, β, γ (deg.)90.000, 103.200, 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 (domestic 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-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
#5: 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 , 7 types, 427 molecules

#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-CA / CALCIUM ION


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


Mass: 126.904 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / 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: Ammonium Iodide, PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.99→39.11 Å / Num. obs: 40499 / % possible obs: 92.62 % / Redundancy: 4.5 % / Rsym value: 0.054 / Net I/σ(I): 9.8
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2891 / Rsym value: 0.495

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.995→39.105 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: FREE R-VALUE / ESU R: 0.244 / ESU R Free: 0.205
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2645 2014 4.973 %
Rwork0.2095 38485 -
all0.212 --
obs-40499 92.622 %
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: 51.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.021 Å20 Å20.004 Å2
2--0.006 Å20 Å2
3---0.012 Å2
Refinement stepCycle: LAST / Resolution: 1.995→39.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 167 397 5334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125070
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164715
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.8496878
X-RAY DIFFRACTIONr_angle_other_deg1.5111.77510859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1485596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.695538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77810827
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.50410239
X-RAY DIFFRACTIONr_chiral_restr0.0770.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026016
X-RAY DIFFRACTIONr_gen_planes_other0.0270.021225
X-RAY DIFFRACTIONr_nbd_refined0.2260.21235
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.24807
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22439
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0990.22639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.2346
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1970.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2330.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.220
X-RAY DIFFRACTIONr_nbd_other0.2540.273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.28
X-RAY DIFFRACTIONr_mcbond_it4.3585.392391
X-RAY DIFFRACTIONr_mcbond_other4.3345.3922384
X-RAY DIFFRACTIONr_mcangle_it6.629.6872975
X-RAY DIFFRACTIONr_mcangle_other6.629.6922976
X-RAY DIFFRACTIONr_scbond_it4.5985.7872679
X-RAY DIFFRACTIONr_scbond_other4.5975.7882680
X-RAY DIFFRACTIONr_scangle_it7.03710.5043902
X-RAY DIFFRACTIONr_scangle_other7.03610.5043903
X-RAY DIFFRACTIONr_lrange_it12.30555.8585997
X-RAY DIFFRACTIONr_lrange_other12.29955.8615996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.0470.3641460.3412891X-RAY DIFFRACTION95.2934
2.047-2.1030.3131580.2922977X-RAY DIFFRACTION99.9362
2.103-2.1630.3391450.2892890X-RAY DIFFRACTION99.9013
2.163-2.230.39870.3461663X-RAY DIFFRACTION59.1616
2.23-2.3030.744920.7271702X-RAY DIFFRACTION62.0976
2.303-2.3830.3481300.2592625X-RAY DIFFRACTION99.4944
2.383-2.4730.3391290.2242546X-RAY DIFFRACTION99.1843
2.473-2.5730.3031250.2172435X-RAY DIFFRACTION99.4561
2.573-2.6870.2621200.2152331X-RAY DIFFRACTION99.3112
2.687-2.8180.3041150.1982230X-RAY DIFFRACTION99.5754
2.818-2.9690.2281070.1782161X-RAY DIFFRACTION99.4737
2.969-3.1480.3121080.2022005X-RAY DIFFRACTION99.529
3.148-3.3640.2711100.1911903X-RAY DIFFRACTION99.1137
3.364-3.6310.261800.1941496X-RAY DIFFRACTION84.233
3.631-3.9750.226860.1761412X-RAY DIFFRACTION87.1437
3.975-4.4380.148790.1331462X-RAY DIFFRACTION97.9034
4.438-5.1140.158750.121277X-RAY DIFFRACTION97.971
5.114-6.2360.205620.1531110X-RAY DIFFRACTION98.8196
6.236-8.7090.222440.151882X-RAY DIFFRACTION99.7845
8-100.202160.161487X-RAY DIFFRACTION90.7942

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