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- PDB-7ve3: Structure of the complex of sheep lactoperoxidase with hypoiodite... -

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Basic information

Entry
Database: PDB / ID: 7ve3
TitleStructure of the complex of sheep lactoperoxidase with hypoiodite at 2.70 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase
Function / homology
Function and homology information


thiocyanate peroxidase activity / peroxidase / response to oxidative stress / defense response to bacterium / heme binding / extracellular space / metal ion binding
Similarity search - Function
Lactoperoxidase / 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
hypoiodous acid / PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / Lactoperoxidase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, P.K. / Yamini, S. / Singh, R.P. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2022
Title: Structural evidence of the oxidation of iodide ion into hyper-reactive hypoiodite ion by mammalian heme lactoperoxidase.
Authors: Singh, P.K. / Ahmad, N. / Yamini, S. / Singh, R.P. / Singh, A.K. / Sharma, P. / Smith, M.L. / Sharma, S. / Singh, T.P.
History
DepositionSep 7, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 22, 2021ID: 3R5Q
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)71,23623
Polymers67,6961
Non-polymers3,53922
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-28 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.942, 80.179, 76.122
Angle α, β, γ (deg.)90.000, 102.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 3 molecules A

#1: Protein Lactoperoxidase


Mass: 67696.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ovis aries (sheep) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9MZY2, peroxidase
#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.: 2 / 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 , 6 types, 177 molecules

#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.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-61D / hypoiodous acid


Mass: 143.912 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: HIO / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: Ammonium iodide, PEG 3350, pH6.8 / PH range: 5-8

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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: MARRESEARCH / Detector: CCD / Date: Feb 13, 2011 / 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: 2.7→43.974 Å / Num. obs: 17167 / % possible obs: 98.1 % / Redundancy: 4.2 % / Rsym value: 0.07 / Net I/σ(I): 46
Reflection shellResolution: 2.7→2.75 Å / Mean I/σ(I) obs: 10 / Num. unique obs: 1120 / Rsym value: 0.24 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IKC

2ikc


Resolution: 2.7→43.974 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.196 / Average fsc free: 0.8624 / Average fsc work: 0.9061 / Cross valid method: FREE R-VALUE / ESU R Free: 0.427
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2769 860 5.032 %
Rwork0.1947 16232 -
all0.199 --
obs-17092 97.635 %
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: 68.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.164 Å20 Å2-0.001 Å2
2---0.284 Å20 Å2
3---0.406 Å2
Refinement stepCycle: LAST / Resolution: 2.7→43.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 62 157 5025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0124997
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.6636786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3365596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15421.601281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.45915825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2081541
X-RAY DIFFRACTIONr_chiral_restr0.1180.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023869
X-RAY DIFFRACTIONr_nbd_refined0.2340.22505
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2198
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3420.21
X-RAY DIFFRACTIONr_mcbond_it4.9496.8582384
X-RAY DIFFRACTIONr_mcangle_it7.83410.2762980
X-RAY DIFFRACTIONr_scbond_it5.2346.862613
X-RAY DIFFRACTIONr_scangle_it7.65510.2213806
X-RAY DIFFRACTIONr_lrange_it13.467124.1321699
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
2.7-2.770.35640.27711200.28112850.7870.83692.14010.226
2.77-2.8450.406650.25611500.26312650.7860.86596.04740.209
2.845-2.9270.376670.22611000.23411950.7930.88597.65690.187
2.927-3.0170.342580.23511210.2411920.8410.8898.90940.206
3.017-3.1150.364650.25610670.26311420.8420.85999.12430.218
3.115-3.2240.389510.24610450.25211050.8090.87899.18550.217
3.224-3.3450.28600.21610050.21910760.8680.90398.97770.199
3.345-3.4810.329560.2229580.22810210.8660.9199.31440.206
3.481-3.6350.327530.2149270.2199880.8710.91899.19030.207
3.635-3.8110.297500.1898890.1949520.890.92998.63450.188
3.811-4.0150.267370.1788440.1828970.9070.93598.21630.183
4.015-4.2570.207340.1737880.1758510.9290.93796.59220.177
4.257-4.5480.238410.1547440.1598100.9240.94796.91360.161
4.548-4.9080.263280.1427000.1467520.920.9696.80850.155
4.908-5.3690.2310.1786500.1797040.9420.94896.7330.194
5.369-5.9920.272250.2065910.2096260.890.92998.40260.229
5.992-6.8970.247250.2085420.215680.920.92599.82390.226
6.897-8.3960.161170.1554440.1554660.9680.96298.9270.176
8.396-11.6630.231230.143320.1463730.9550.97395.17430.163
11.663-43.9740.242100.2162150.2172340.9380.9596.15380.267

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