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- PDB-9ku6: Crystal structure of the complex of lactoperoxidase with nitric o... -

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Basic information

Entry
Database: PDB / ID: 9ku6
TitleCrystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Bovine lactoperoxidase / Peroxide family
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane / 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 / NITRIC OXIDE / NITRITE ION / TRIETHYLENE GLYCOL / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsMaurya, A. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Indian Council of Medical ResearchIR-661 India
CitationJournal: To Be Published
Title: Crystal structure of the complex of lactoperoxidase with nitric oxide at 1.72 A resolution
Authors: Maurya, A. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: 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)73,88553
Polymers67,8051
Non-polymers6,08052
Water9,386521
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)54.020, 80.405, 75.844
Angle α, β, γ (deg.)90.000, 103.117, 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: 67805.305 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
#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 / 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, 569 molecules

#4: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2 / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: 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
#10: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 8 / Details: 0.2M AMMONIUM IODIDE, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.72→73.86 Å / Num. obs: 66501 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 36 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.8
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3455 / CC1/2: 0.65 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→73.86 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.235 1320 1.987 %
Rwork0.1859 65119 -
all0.187 --
obs-66439 99.039 %
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: 48.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.014 Å2-0 Å20.019 Å2
2---0.021 Å20 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.72→73.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4772 0 209 521 5502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125112
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164721
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.856913
X-RAY DIFFRACTIONr_angle_other_deg1.5571.77410875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3055598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.268538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84410828
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.32710241
X-RAY DIFFRACTIONr_chiral_restr0.0820.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026043
X-RAY DIFFRACTIONr_gen_planes_other0.0270.021234
X-RAY DIFFRACTIONr_nbd_refined0.2420.21246
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.24875
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1030.22604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2441
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1260.25
X-RAY DIFFRACTIONr_metal_ion_refined0.6810.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.221
X-RAY DIFFRACTIONr_nbd_other0.2540.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.221
X-RAY DIFFRACTIONr_mcbond_it4.5445.0862408
X-RAY DIFFRACTIONr_mcbond_other4.5055.0962389
X-RAY DIFFRACTIONr_mcangle_it6.8489.1462983
X-RAY DIFFRACTIONr_mcangle_other6.8489.1512984
X-RAY DIFFRACTIONr_scbond_it4.9515.4672704
X-RAY DIFFRACTIONr_scbond_other4.955.4672705
X-RAY DIFFRACTIONr_scangle_it7.6439.9113929
X-RAY DIFFRACTIONr_scangle_other7.6429.9123930
X-RAY DIFFRACTIONr_lrange_it12.58955.576144
X-RAY DIFFRACTIONr_lrange_other12.58855.5726143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7650.549850.4814752X-RAY DIFFRACTION98.034
1.765-1.8130.4940.44621X-RAY DIFFRACTION98.127
1.813-1.8660.436880.3884547X-RAY DIFFRACTION98.1784
1.866-1.9230.3681000.3624371X-RAY DIFFRACTION99.0035
1.923-1.9860.321860.3214288X-RAY DIFFRACTION99.0714
1.986-2.0560.343910.2824139X-RAY DIFFRACTION98.878
2.056-2.1330.302740.2553990X-RAY DIFFRACTION98.953
2.133-2.220.326810.2413838X-RAY DIFFRACTION98.9397
2.22-2.3190.28860.2183694X-RAY DIFFRACTION99.1866
2.319-2.4320.272820.2073533X-RAY DIFFRACTION99.3405
2.432-2.5630.243760.1873373X-RAY DIFFRACTION99.3376
2.563-2.7180.279630.1763192X-RAY DIFFRACTION99.3893
2.718-2.9060.241660.1673015X-RAY DIFFRACTION99.7087
2.906-3.1380.235540.1782806X-RAY DIFFRACTION99.7558
3.138-3.4370.232420.1752613X-RAY DIFFRACTION99.6996
3.437-3.8420.203460.1682358X-RAY DIFFRACTION99.8754
3.842-4.4340.187460.1322069X-RAY DIFFRACTION99.9055
4.434-5.4260.126240.1191768X-RAY DIFFRACTION99.2248
5.426-7.6530.168260.1371373X-RAY DIFFRACTION99.9286
7.653-100.153100.153778X-RAY DIFFRACTION98.6233

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