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- PDB-7de5: Crystal structure of yak lactoperoxidase at 1.55 A resolution. -

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Basic information

Entry
Database: PDB / ID: 7de5
TitleCrystal structure of yak lactoperoxidase at 1.55 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase
Function / homology
Function and homology information


thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / basolateral plasma membrane / response to oxidative stress / defense response to bacterium / heme binding / extracellular space / metal ion binding / 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 / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus grunniens (domestic yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSingh, P.K. / Viswanathan, V. / Sharma, P. / Rani, C. / Ahmad, N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Protein J. / Year: 2021
Title: Structure of Yak Lactoperoxidase at 1.55 angstrom Resolution.
Authors: Viswanathan, V. / Rani, C. / Ahmad, N. / Singh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionNov 2, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionNov 25, 2020ID: 7CH2
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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

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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)75,16448
Polymers67,7731
Non-polymers7,39047
Water11,205622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.910, 78.980, 67.820
Angle α, β, γ (deg.)90.000, 92.960, 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: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos mutus grunniens (domestic yak) / References: UniProt: L8ICE9, peroxidase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: 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 / 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, 665 molecules

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


Mass: 126.904 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: I
#7: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M AMMONIUM IODIDE, 20% PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K
PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 9, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.55→44.53 Å / Num. obs: 81152 / % possible obs: 98.4 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.067 / Net I/σ(I): 7.6
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5535 / CC1/2: 0.44 / Rpim(I) all: 0.604 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BYZ

7byz
PDB Unreleased entry


Resolution: 1.55→43.247 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.444 / SU ML: 0.083 / Cross valid method: FREE R-VALUE / ESU R: 0.093 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.226 1676 2.069 %
Rwork0.1865 79336 -
all0.187 --
obs-81012 98.406 %
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: 19.578 Å2
Baniso -1Baniso -2Baniso -3
1--0.008 Å2-0 Å2-0.015 Å2
2---0.005 Å20 Å2
3---0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.55→43.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 226 622 5618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135213
X-RAY DIFFRACTIONr_bond_other_d0.0060.0174865
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.6967099
X-RAY DIFFRACTIONr_angle_other_deg1.4911.61711232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4085624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66121.773282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2815858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9351539
X-RAY DIFFRACTIONr_chiral_restr0.0850.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025833
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021251
X-RAY DIFFRACTIONr_nbd_refined0.2150.21149
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24894
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22508
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.22212
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2466
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.24
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4610.239
X-RAY DIFFRACTIONr_nbd_other0.4740.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2540.240
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1990.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.7740.21
X-RAY DIFFRACTIONr_mcbond_it1.9751.9112414
X-RAY DIFFRACTIONr_mcbond_other1.9341.9072408
X-RAY DIFFRACTIONr_mcangle_it3.1652.8533017
X-RAY DIFFRACTIONr_mcangle_other3.1652.8553018
X-RAY DIFFRACTIONr_scbond_it2.012.1252799
X-RAY DIFFRACTIONr_scbond_other2.012.1252800
X-RAY DIFFRACTIONr_scangle_it3.0953.1224067
X-RAY DIFFRACTIONr_scangle_other3.0943.1234068
X-RAY DIFFRACTIONr_lrange_it5.79123.736205
X-RAY DIFFRACTIONr_lrange_other5.7923.7316206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.2891400.2895535X-RAY DIFFRACTION93.0938
1.59-1.6340.3011200.2945453X-RAY DIFFRACTION94.5538
1.634-1.6810.3241170.275390X-RAY DIFFRACTION95.874
1.681-1.7330.2481020.2475310X-RAY DIFFRACTION97.2507
1.733-1.7890.2631220.2225190X-RAY DIFFRACTION98.3158
1.789-1.8520.2291140.2095087X-RAY DIFFRACTION99.1422
1.852-1.9220.261830.2324955X-RAY DIFFRACTION99.5849
1.922-20.241980.1934756X-RAY DIFFRACTION99.9382
2-2.0890.231960.1854556X-RAY DIFFRACTION100
2.089-2.190.238810.1754385X-RAY DIFFRACTION100
2.19-2.3090.242980.1964159X-RAY DIFFRACTION99.9296
2.309-2.4480.201710.1553947X-RAY DIFFRACTION99.9751
2.448-2.6170.184810.1463693X-RAY DIFFRACTION100
2.617-2.8250.231730.1683496X-RAY DIFFRACTION100
2.825-3.0940.233580.1633157X-RAY DIFFRACTION100
3.094-3.4570.18570.1562882X-RAY DIFFRACTION100
3.457-3.9870.163480.1492581X-RAY DIFFRACTION100
3.987-4.8730.179500.1472157X-RAY DIFFRACTION100
4.873-6.8480.276540.1941684X-RAY DIFFRACTION100
6.848-100.183130.183963X-RAY DIFFRACTION98.7854

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