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- PDB-7dn7: Crystal structure of ternary complexes of lactoperoxidase with hy... -

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Basic information

Entry
Database: PDB / ID: 7dn7
TitleCrystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / lactoperoxidase
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 / 1-(OXIDOSULFANYL)METHANAMINE / HYDROGEN PEROXIDE / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSingh, P.K. / Singh, A.K. / Singh, R.P. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: J.Inorg.Biochem. / Year: 2021
Title: Structure of a ternary complex of lactoperoxidase with iodide and hydrogen peroxide at 1.77 angstrom resolution.
Authors: Singh, P.K. / Sharma, P. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 30, 2020ID: 6LAQ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 1.3Oct 16, 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

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Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,10731
Polymers67,7731
Non-polymers4,33330
Water11,872659
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-37 kcal/mol
Surface area24310 Å2
Unit cell
Length a, b, c (Å)53.920, 79.498, 77.723
Angle α, β, γ (deg.)90.000, 102.250, 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, 3 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
#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.: 2 / 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 , 8 types, 686 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
#6: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH5NOS
#10: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.4 Å3/Da / Density % sol: 48.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Ammonium Iodide, PEG 3350 / 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: Oct 21, 2010 / Details: Mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→75.9 Å / Num. obs: 67857 / % possible obs: 96 % / Redundancy: 9.2 % / Rsym value: 0.068 / Net I/σ(I): 11
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 4718 / Rsym value: 0.33 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ql6

3ql6
PDB Unreleased entry


Resolution: 1.7→26.707 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.118 / ESU R Free: 0.107
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2043 3384 5.051 %
Rwork0.1814 63610 -
all0.183 --
obs-66994 94.999 %
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: 29.047 Å2
Baniso -1Baniso -2Baniso -3
1-0.018 Å2-0 Å20.014 Å2
2---0.046 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 138 659 5567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135072
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174739
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.686894
X-RAY DIFFRACTIONr_angle_other_deg2.5611.60510909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2615602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54221.673281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88515837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0091540
X-RAY DIFFRACTIONr_chiral_restr0.0970.2629
X-RAY DIFFRACTIONr_chiral_restr_other2.9660.23
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025751
X-RAY DIFFRACTIONr_gen_planes_other0.020.021236
X-RAY DIFFRACTIONr_nbd_refined0.220.21147
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.24751
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22436
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22255
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2471
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.140.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0970.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3070.215
X-RAY DIFFRACTIONr_nbd_other0.2440.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1350.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0340.21
X-RAY DIFFRACTIONr_mcbond_it3.1592.8452402
X-RAY DIFFRACTIONr_mcbond_other3.1342.842398
X-RAY DIFFRACTIONr_mcangle_it5.0494.2543007
X-RAY DIFFRACTIONr_mcangle_other5.0424.2573005
X-RAY DIFFRACTIONr_scbond_it3.4083.1272670
X-RAY DIFFRACTIONr_scbond_other3.4073.1282671
X-RAY DIFFRACTIONr_scangle_it5.2884.593887
X-RAY DIFFRACTIONr_scangle_other5.2874.5923888
X-RAY DIFFRACTIONr_lrange_it10.28653.21427433
X-RAY DIFFRACTIONr_lrange_other10.28753.21427430
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
1.7-1.7440.2482610.21547180.21751830.9090.91796.06410.182
1.744-1.7910.2332360.20646080.20850140.9190.92896.60950.173
1.791-1.8430.2632220.21545470.21749350.9030.9296.63630.182
1.843-1.90.3182220.25841170.26147460.8740.89591.42440.207
1.9-1.9610.3451980.31241890.31446310.8230.84594.73120.279
1.961-2.030.2352270.19240950.19444620.930.94496.86240.168
2.03-2.1060.2082130.18540120.18643290.9450.94997.59760.169
2.106-2.1920.2121800.18638260.18741400.940.94396.76330.167
2.192-2.2880.2921810.25933060.26140080.8840.90387.0010.239
2.288-2.3990.2011870.16935050.1738270.9460.95596.47240.155
2.399-2.5280.1721870.15334000.15436550.960.96398.13950.147
2.528-2.680.21730.15732090.15934320.9520.9698.54310.154
2.68-2.8620.1881750.16830010.16932280.9560.95798.38910.17
2.862-3.0890.1941590.16828160.1730200.9530.95898.50990.174
3.089-3.3790.1641400.1626250.1627980.9670.96698.82060.171
3.379-3.7710.1671230.16220900.16225080.9640.96488.23760.174
3.771-4.3390.154840.14115450.14122530.970.97172.30360.16
4.339-5.280.1681040.14717960.14819260.9680.97198.650.179
5.28-7.3250.199740.17214080.17414960.9470.95599.06420.209
7.325-26.7070.232380.1867970.1889110.9070.94591.65750.23

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