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- PDB-6lqw: Crystal structure of a dimeric yak lactoperoxidase at 2.59 A reso... -

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Basic information

Entry
Database: PDB / ID: 6lqw
TitleCrystal structure of a dimeric yak lactoperoxidase at 2.59 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxide family
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
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 / HYDROGEN PEROXIDE / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsViswanathan, V. / Pandey, S.N. / Ahmad, N. / Rani, C. / Sharma, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)PDF/2018/000008 India
CitationJournal: To Be Published
Title: Crystal structure of a dimeric yak lactoperoxidase at 2.59 A resolution.
Authors: Viswanathan, V. / Pandey, S.N. / Sharma, P. / Rani, C. / Ahmad, N. / Sharma, S. / Singh, T.P.
History
DepositionJan 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2020Provider: 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 / struct_site / struct_site_gen
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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 29, 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
B: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,76818
Polymers135,5472
Non-polymers3,22216
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-24 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.295, 96.732, 83.931
Angle α, β, γ (deg.)90.000, 90.304, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Sugars , 2 types, 10 molecules AB

#1: Protein Lactoperoxidase /


Mass: 67773.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos mutus (wild yak) / References: UniProt: L8ICE9
#2: 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.: 8
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, 264 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2M Ammonium formate, 20% PEG 3350

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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: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.59→40.64 Å / Num. obs: 40278 / % possible obs: 98.74 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.31 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.072 / Rrim(I) all: 0.14 / Net I/σ(I): 6.5
Reflection shellResolution: 2.59→2.67 Å / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3537 / CC1/2: 0.84 / Rpim(I) all: 0.266 / Rrim(I) all: 0.521 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L3Z

6l3z
PDB Unreleased entry


Resolution: 2.6→40.64 Å / SU ML: 0.4379 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.9451
RfactorNum. reflection% reflection
Rfree0.2923 1058 2.64 %
Rwork0.2116 --
obs0.2137 40090 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.19 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9540 0 206 256 10002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009110046
X-RAY DIFFRACTIONf_angle_d1.109413676
X-RAY DIFFRACTIONf_chiral_restr0.0551446
X-RAY DIFFRACTIONf_plane_restr0.00821779
X-RAY DIFFRACTIONf_dihedral_angle_d5.2167147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.36121410.26734779X-RAY DIFFRACTION98.28
2.72-2.860.32771490.24454835X-RAY DIFFRACTION99.96
2.86-3.040.31381050.23354893X-RAY DIFFRACTION99.98
3.04-3.270.34771320.22864873X-RAY DIFFRACTION100
3.27-3.60.31831320.20514880X-RAY DIFFRACTION100
3.6-4.120.26411120.18434903X-RAY DIFFRACTION99.98
4.12-5.20.23041470.18584891X-RAY DIFFRACTION100
5.2-58.240.28881400.21684978X-RAY DIFFRACTION99.77

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