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- PDB-7dmr: Crystal structure of potassium induced heme modification in yak l... -

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Basic information

Entry
Database: PDB / ID: 7dmr
TitleCrystal structure of potassium induced heme modification in yak lactoperoxidase at 2.20 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 / peroxidase / lactoperoxidase activity / response to oxidative stress / basolateral plasma membrane / defense response to bacterium / heme binding / extracellular space / metal ion binding / cytoplasm
Similarity search - Function
Myeloperoxidase, subunit C / Haem peroxidase domain superfamily, animal type / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSingh, P.K. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2021
Title: Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution.
Authors: Singh, P.K. / Pandey, S. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionDec 6, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionDec 16, 2020ID: 6L41
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 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 1.2Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Revision 1.4Oct 23, 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)69,72311
Polymers67,7731
Non-polymers1,95010
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-65 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.240, 85.310, 98.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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 (wild yak) / References: UniProt: L8ICE9, 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-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
#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
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, 458 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M potassium fluoride, 20% PEG 3350 / PH range: 5-8 / Temp details: 100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2019 / Details: mirror
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→64.61 Å / Num. obs: 35146 / % possible obs: 99.9 % / Redundancy: 12 % / CC1/2: 0.993 / Rsym value: 0.2 / Net I/σ(I): 9.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2386 / CC1/2: 0.764 / Rsym value: 0.914 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BXI

3bxi


Resolution: 2.2→64.606 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.848 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.285 / ESU R Free: 0.218
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2427 1815 5.179 %
Rwork0.1896 33233 -
all0.192 --
obs-35048 99.71 %
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: 30.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.054 Å2-0 Å20 Å2
2--0.09 Å2-0 Å2
3----0.036 Å2
Refinement stepCycle: LAST / Resolution: 2.2→64.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 118 452 5340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135053
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174689
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6866861
X-RAY DIFFRACTIONr_angle_other_deg1.291.60710802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4565594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86721.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72915825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8941538
X-RAY DIFFRACTIONr_chiral_restr0.0750.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025709
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021221
X-RAY DIFFRACTIONr_nbd_refined0.2180.21109
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.24484
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22411
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22246
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2353
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.22
X-RAY DIFFRACTIONr_metal_ion_refined0.4190.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1190.210
X-RAY DIFFRACTIONr_nbd_other0.2580.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.29
X-RAY DIFFRACTIONr_mcbond_it2.3723.0832382
X-RAY DIFFRACTIONr_mcbond_other2.3553.082381
X-RAY DIFFRACTIONr_mcangle_it3.934.6142972
X-RAY DIFFRACTIONr_mcangle_other3.9314.6192973
X-RAY DIFFRACTIONr_scbond_it2.5123.352669
X-RAY DIFFRACTIONr_scbond_other2.5113.3512670
X-RAY DIFFRACTIONr_scangle_it4.0384.933889
X-RAY DIFFRACTIONr_scangle_other4.0384.9313890
X-RAY DIFFRACTIONr_lrange_it8.71858.57525640
X-RAY DIFFRACTIONr_lrange_other8.71758.57625640
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
2.2-2.2570.3751320.38623860.38525430.5590.55799.01690.339
2.257-2.3190.331110.30223660.30325030.7240.75498.96120.261
2.319-2.3860.2691360.24422750.24524220.8420.85499.54580.199
2.386-2.4590.281220.2322210.23223530.8440.86799.5750.186
2.459-2.540.2781380.21121440.21522860.880.89199.8250.171
2.54-2.6290.2691080.19721190.20122280.8820.91199.95510.161
2.629-2.7280.2711070.20120390.20521470.8890.91599.95340.165
2.728-2.8390.3141170.18219570.18920770.8730.92399.85560.151
2.839-2.9650.2351020.16718740.1719760.9230.9371000.141
2.965-3.110.235960.17518090.17919050.9270.941000.148
3.11-3.2770.218860.1717330.17218190.9350.9431000.147
3.277-3.4760.231830.17716240.17917120.930.94899.70790.159
3.476-3.7150.194870.16815280.16916160.950.95599.93810.151
3.715-4.0110.276630.17114520.17615210.9270.9599.60550.157
4.011-4.3920.225650.14813420.15214080.9380.95799.9290.14
4.392-4.9080.19790.14611930.14912720.9560.9671000.139
4.908-5.6620.226730.1610620.16411360.9490.96999.9120.151
5.662-6.9210.224490.1799260.1819750.9470.9641000.17
6.921-9.7320.125480.1347300.1347790.9830.9899.87160.135
9.732-64.6060.272130.1954530.1974720.9560.96798.72880.198

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