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- PDB-6kmk: Crystal structure of hydrogen peroxide bound bovine lactoperoxida... -

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Basic information

Entry
Database: PDB / ID: 6kmk
TitleCrystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase / Hydrogen peroxide
Function / homology
Function and homology information


Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / calcium ion binding ...Events associated with phagocytolytic activity of PMN cells / thiocyanate peroxidase activity / lactoperoxidase activity / peroxidase / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / response to oxidative stress / defense response to bacterium / calcium ion binding / heme binding / extracellular space / 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 / IODIDE ION / HYDROGEN PEROXIDE / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSingh, P.K. / Sirohi, H.V. / Bhusan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of hydrogen peroxide bound bovine lactoperoxidase at 2.3 A resolution
Authors: Singh, P.K. / Sirohi, H.V. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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)71,36624
Polymers67,8531
Non-polymers3,51323
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-6 kcal/mol
Surface area24770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.828, 80.420, 75.823
Angle α, β, γ (deg.)90.000, 102.577, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Lactoperoxidase / LPO


Mass: 67853.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80025, peroxidase
#4: 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.: 4
Source method: isolated from a genetically manipulated source
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, 270 molecules

#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.2M AMMONIUM IODIDE, 20% PEG3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP, 298K.
PH range: 6-8

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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: 0.9795 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→54.515 Å / Num. obs: 27946 / % possible obs: 99.2 % / Redundancy: 3.4 % / CC1/2: 0.96 / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2 / Num. unique obs: 2737 / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
AUTOMARdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NT3

4nt3
PDB Unreleased entry


Resolution: 2.3→54.46 Å / Cor.coef. Fo:Fc: 0.852 / Cor.coef. Fo:Fc free: 0.82 / SU B: 10.255 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.306
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2951 1401 5.04 %
Rwork0.2454 --
all0.248 --
obs-27800 98.725 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.537 Å2
Baniso -1Baniso -2Baniso -3
1-0.617 Å2-0 Å2-1.481 Å2
2---1.246 Å2-0 Å2
3---1.174 Å2
Refinement stepCycle: LAST / Resolution: 2.3→54.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4774 0 119 251 5144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135029
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174558
X-RAY DIFFRACTIONr_angle_refined_deg1.511.686836
X-RAY DIFFRACTIONr_angle_other_deg1.2061.59810590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8635594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96221.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74115824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0931538
X-RAY DIFFRACTIONr_chiral_restr0.0680.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025608
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021099
X-RAY DIFFRACTIONr_nbd_refined0.2210.21254
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24804
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22366
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.22167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2273
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.225
X-RAY DIFFRACTIONr_nbd_other0.2990.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.270.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0750.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.7360.21
X-RAY DIFFRACTIONr_mcbond_it2.9984.312382
X-RAY DIFFRACTIONr_mcbond_other2.9934.3072381
X-RAY DIFFRACTIONr_mcangle_it4.76.4552972
X-RAY DIFFRACTIONr_mcangle_other4.76.4582973
X-RAY DIFFRACTIONr_scbond_it2.7634.4742647
X-RAY DIFFRACTIONr_scbond_other2.7614.4742647
X-RAY DIFFRACTIONr_scangle_it4.3286.6523864
X-RAY DIFFRACTIONr_scangle_other4.3286.6523865
X-RAY DIFFRACTIONr_lrange_it7.09949.2265894
X-RAY DIFFRACTIONr_lrange_other7.10149.2255893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.3171010.191999X-RAY DIFFRACTION100
2.36-2.4240.292960.191883X-RAY DIFFRACTION100
2.424-2.4950.285950.191875X-RAY DIFFRACTION100
2.495-2.5710.3151090.191792X-RAY DIFFRACTION99.9474
2.571-2.6550.249920.191738X-RAY DIFFRACTION99.9454
2.655-2.7480.334900.191714X-RAY DIFFRACTION99.7788
2.748-2.8520.305800.191649X-RAY DIFFRACTION99.9422
2.852-2.9680.304730.191591X-RAY DIFFRACTION100
2.968-3.10.2731020.191478X-RAY DIFFRACTION99.9367
3.1-3.2510.26860.191440X-RAY DIFFRACTION99.9345
3.251-3.4270.346620.191350X-RAY DIFFRACTION96.4481
3.427-3.6340.424590.191269X-RAY DIFFRACTION96.6521
3.634-3.8840.27540.191118X-RAY DIFFRACTION90.8527
3.884-4.1950.231580.191037X-RAY DIFFRACTION89.3878
4.195-4.5930.193570.1591048X-RAY DIFFRACTION100
4.593-5.1330.202660.152941X-RAY DIFFRACTION100
5.133-5.9220.336440.191860X-RAY DIFFRACTION100
5.922-7.2420.219380.19711X-RAY DIFFRACTION100
7.242-100.225290.168573X-RAY DIFFRACTION100
8-100.219100.19333X-RAY DIFFRACTION99.1329

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