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- PDB-7y3u: Crystal structure of the complex of Lactoperoxidase with Nitric o... -

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Basic information

Entry
Database: PDB / ID: 7y3u
TitleCrystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A 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
ACETATE ION / Mesoheme / NITRIC OXIDE / Lactoperoxidase
Similarity search - Component
Biological speciesBos grunniens (domestic yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSingh, P.K. / Viswanathan, V. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution
Authors: Singh, P.K. / Viswanathan, V. / Ahmad, N.
History
DepositionJun 13, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 29, 2022ID: 6LRN
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactoperoxidase
B: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,52318
Polymers135,5472
Non-polymers3,97616
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-4 kcal/mol
Surface area47210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.731, 93.173, 82.319
Angle α, β, γ (deg.)90.000, 91.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Auth seq-ID: 1 - 595 / Label seq-ID: 1 - 595

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lactoperoxidase


Mass: 67773.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos grunniens (domestic yak) / References: UniProt: L8ICE9, peroxidase

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Sugars , 2 types, 8 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: 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.: 6 / 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, 193 molecules

#3: Chemical ChemComp-MH0 / Mesoheme


Mass: 620.519 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H36FeN4O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: 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
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.3 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M cacl2, 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: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.5→48.911 Å / Num. obs: 42834 / % possible obs: 99 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2923 / CC1/2: 0.638 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LRN

6lrn
PDB Unreleased entry


Resolution: 2.5→48.864 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.908 / Cross valid method: FREE R-VALUE / ESU R: 3.107 / ESU R Free: 0.353
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2774 2105 4.968 %
Rwork0.219 40267 -
all0.222 --
obs-42372 98.924 %
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: 59.307 Å2
Baniso -1Baniso -2Baniso -3
1--0.154 Å2-0 Å2-0.015 Å2
2---0.088 Å2-0 Å2
3---0.243 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9542 0 259 185 9986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01310109
X-RAY DIFFRACTIONr_bond_other_d0.0340.0159389
X-RAY DIFFRACTIONr_angle_refined_deg1.5061.68813745
X-RAY DIFFRACTIONr_angle_other_deg2.4531.60921634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74951188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80421.841554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.038151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4881576
X-RAY DIFFRACTIONr_chiral_restr0.060.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211410
X-RAY DIFFRACTIONr_gen_planes_other0.0190.022439
X-RAY DIFFRACTIONr_nbd_refined0.2090.22236
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.29255
X-RAY DIFFRACTIONr_nbtor_refined0.1610.24740
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.24540
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2326
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.213
X-RAY DIFFRACTIONr_metal_ion_refined0.1460.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2410.228
X-RAY DIFFRACTIONr_nbd_other0.210.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0570.22
X-RAY DIFFRACTIONr_mcbond_it4.5696.194767
X-RAY DIFFRACTIONr_mcbond_other4.5686.1884764
X-RAY DIFFRACTIONr_mcangle_it7.2859.2785944
X-RAY DIFFRACTIONr_mcangle_other7.2849.2815945
X-RAY DIFFRACTIONr_scbond_it3.9396.4595342
X-RAY DIFFRACTIONr_scbond_other3.9386.465342
X-RAY DIFFRACTIONr_scangle_it6.3539.5967800
X-RAY DIFFRACTIONr_scangle_other6.3539.5977801
X-RAY DIFFRACTIONr_lrange_it12.434113.60643877
X-RAY DIFFRACTIONr_lrange_other12.434113.63443843
X-RAY DIFFRACTIONr_ncsr_local_group_10.0930.0519661
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.093260.05009
12BX-RAY DIFFRACTIONLocal ncs0.093260.05009
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
2.5-2.5650.3621480.32729230.32931180.6620.70298.49260.311
2.565-2.6350.3691670.32228680.32530750.7090.69598.69920.307
2.635-2.7110.3831580.31427680.31829700.6720.71198.51850.293
2.711-2.7940.3271530.30327160.30529070.7790.77798.69280.274
2.794-2.8850.3621700.27326080.27828140.7360.80498.72070.248
2.885-2.9860.3231130.2525530.25326970.8150.85898.85060.223
2.986-3.0990.3511090.24725160.25126570.8180.8798.79560.223
3.099-3.2250.338770.26524010.26825000.8260.84499.120.243
3.225-3.3670.3271420.23822720.24324380.8320.88799.01560.215
3.367-3.5310.2941140.23221760.23523090.8780.89999.17710.21
3.531-3.7210.295970.2221230.22322380.8810.91599.19570.204
3.721-3.9450.2381330.19319350.19620860.9180.93699.13710.178
3.945-4.2160.2461090.17918380.18319600.930.94299.33670.168
4.216-4.550.257790.17517530.17818450.9230.94199.29540.166
4.55-4.980.247790.1816080.18316950.9220.94199.5280.176
4.98-5.5610.225620.17614570.17815270.9360.95199.47610.173
5.561-6.4080.287660.19213040.19613760.8890.92999.5640.187
6.408-7.8140.215640.17110960.17311670.9420.94499.40020.173
7.814-10.9120.156300.1498600.158980.9720.97599.10910.161
10.912-48.8640.21350.2644920.265490.9460.92395.99270.309

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