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- PDB-7dao: Crystal structure of native yak lactoperoxidase at 2.28 A resolution -

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Basic information

Entry
Database: PDB / ID: 7dao
TitleCrystal structure of native yak lactoperoxidase at 2.28 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 / basolateral plasma membrane / response to oxidative stress / 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: 2.28 Å
AuthorsSingh, P.K. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of native yak lactoperoxidase at 2.28 A resolution
Authors: Singh, P.K. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P.
History
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 13, 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)69,6199
Polymers67,7731
Non-polymers1,8458
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-30 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.162, 85.242, 96.443
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 / 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 , 5 types, 346 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.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.05M potassium fluoride, 20% 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: BM30A / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.28→42.621 Å / Num. obs: 30344 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7
Reflection shellResolution: 2.28→2.34 Å / Mean I/σ(I) obs: 2.28 / Num. unique obs: 2081 / CC1/2: 0.79 / Rrim(I) all: 0.99 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D52

7d52


Resolution: 2.28→42.62 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.643 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / ESU R: 0.313 / ESU R Free: 0.237
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2434 770 2.538 %
Rwork0.1742 29573 -
all0.176 --
obs-30343 98.513 %
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: 50.639 Å2
Baniso -1Baniso -2Baniso -3
1--3.004 Å20 Å2-0 Å2
2---0.967 Å20 Å2
3---3.971 Å2
Refinement stepCycle: LAST / Resolution: 2.28→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 116 342 5228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125034
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.6776852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8365594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66521.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74815825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2471538
X-RAY DIFFRACTIONr_chiral_restr0.1170.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023895
X-RAY DIFFRACTIONr_nbd_refined0.2120.22327
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2294
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.26
X-RAY DIFFRACTIONr_mcbond_it4.3874.8682379
X-RAY DIFFRACTIONr_mcangle_it6.9667.2842972
X-RAY DIFFRACTIONr_scbond_it4.9365.1982655
X-RAY DIFFRACTIONr_scangle_it7.467.6313879
X-RAY DIFFRACTIONr_lrange_it13.92489.50722021
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
2.28-2.3390.42540.33720810.33922270.7610.77495.86890.312
2.339-2.4030.37500.27119010.27321810.830.84489.45440.247
2.403-2.4720.271510.24119470.24121170.8740.87994.37880.21
2.472-2.5480.243520.21920120.21920640.9160.9031000.193
2.548-2.6310.319510.20419510.20720020.8980.9211000.173
2.631-2.7230.259490.18518910.18719410.910.92699.94850.16
2.723-2.8260.281470.19618190.19818660.8890.9131000.171
2.826-2.9410.285460.1917820.19318290.8840.91799.94530.168
2.941-3.0710.277440.19416840.19617280.9060.9211000.176
3.071-3.220.281430.19716260.19916690.90.9261000.184
3.22-3.3930.317400.17715420.1815820.8890.9461000.167
3.393-3.5970.197380.16714760.16815150.9650.95899.9340.16
3.597-3.8440.234360.15813740.1614110.9280.96399.92910.158
3.844-4.1490.197330.14112960.14213300.9490.96899.92480.145
4.149-4.5410.14320.11812030.11912360.9790.97699.91910.124
4.541-5.0690.205280.12410930.12611230.9590.97699.82190.136
5.069-5.840.204250.149690.1419940.9530.9681000.152
5.84-7.1190.158220.168400.168620.9470.9651000.17
7.119-9.930.25180.1596680.1616870.9540.96899.85440.18
9.93-42.6210.342110.2294180.2324320.8870.93599.30560.271

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