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- PDB-4oek: Crystal Structure of the Complex of goat Lactoperoxidase with Phe... -

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Basic information

Entry
Database: PDB / ID: 4oek
TitleCrystal Structure of the Complex of goat Lactoperoxidase with Phenylethylamine at 2.47 A Resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxidase
Function / homology
Function and homology information


thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane ...thiocyanate catabolic process / thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / lactoperoxidase activity / peroxidase / antifungal humoral response / hydrogen peroxide catabolic process / peroxidase activity / antibacterial humoral response / basolateral plasma membrane / response to oxidative stress / 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 / 2-PHENYLETHYLAMINE / THIOCYANATE ION / Lactoperoxidase / Lactoperoxidase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsKumar, M. / Singh, R.P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal Structure of the Complex of goat Lactoperoxidase with Phenylethylamine at 2.47 A
Authors: Kumar, M. / Singh, R.P. / Sinha, M. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.occupancy / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 2.1Sep 20, 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)71,49527
Polymers67,6101
Non-polymers3,88526
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.166, 79.891, 75.284
Angle α, β, γ (deg.)90.00, 101.80, 90.00
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: 67609.766 Da / Num. of mol.: 1 / Fragment: UNP residues 118-712 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat)
References: UniProt: A3F9D6, UniProt: A0A452E9Y6*PLUS, 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-Glycam 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
[]{[(4+1)][b-D-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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 , 7 types, 272 molecules

#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#7: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PEA / 2-PHENYLETHYLAMINE / Phenethylamine


Mass: 122.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N / Comment: alkaloid*YM
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 298 K / pH: 6.8
Details: Sodium nitrate, PEG , pH 6.8 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 2013 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.47→74.21 Å / Num. obs: 18577 / % possible obs: 89.2 % / Observed criterion σ(I): 0 / Rsym value: 0.081 / Net I/σ(I): 26.4
Reflection shellResolution: 2.47→2.54 Å / Mean I/σ(I) obs: 4.9 / Rsym value: 0.299 / % possible all: 91.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SXV

3sxv


Resolution: 2.47→73.69 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.721 / SU ML: 0.228 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 995 5.1 %RANDOM
Rwork0.204 ---
obs0.208 18577 88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.161 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0 Å2-2.22 Å2
2---1.92 Å2-0 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 2.47→73.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 159 250 5166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.025048
X-RAY DIFFRACTIONr_bond_other_d0.0030.023510
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9856861
X-RAY DIFFRACTIONr_angle_other_deg3.0723.0038452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3235594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67723.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10315804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6341538
X-RAY DIFFRACTIONr_chiral_restr0.0780.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215564
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021064
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.47→2.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 69 -
Rwork0.261 1100 -
obs--72.7 %
Refinement TLS params.Method: refined / Origin x: 7.7372 Å / Origin y: -0.5141 Å / Origin z: 21.9791 Å
111213212223313233
T0.022 Å2-0.0068 Å20.0092 Å2-0.0316 Å20.0073 Å2--0.0258 Å2
L0.3919 °20.1675 °20.1289 °2-0.7155 °2-0.1645 °2--0.1785 °2
S-0.0083 Å °0.0194 Å °0.0241 Å °-0.0586 Å °0.0311 Å °0.0788 Å °0.0149 Å °0.0016 Å °-0.0228 Å °

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