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- PDB-4msf: Crystal structure of the complex of goat lactoperoxidase with 3-h... -

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Basic information

Entry
Database: PDB / ID: 4msf
TitleCrystal structure of the complex of goat lactoperoxidase with 3-hydroxymethyl phenol at 1.98 Angstrom 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 / peroxidase activity / hydrogen peroxide catabolic process / 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 / peroxidase activity / hydrogen peroxide catabolic process / 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
3-(hydroxymethyl)phenol / PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Lactoperoxidase / Lactoperoxidase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsSingh, A. / Singh, R.P. / Sinha, M. / Singh, A.K. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be published
Title: Crystal structure of the complex of goat lactoperoxidase with 3-hydroxymethyl phenol at 1.98 Angstrom resolution
Authors: Singh, A. / Singh, R.P. / Sinha, M. / Singh, A.K. / Bhushan, A. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 18, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2013Provider: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 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)71,57328
Polymers67,6101
Non-polymers3,96427
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.766, 80.356, 75.760
Angle α, β, γ (deg.)90.00, 102.71, 90.00
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 /


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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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 , 8 types, 527 molecules

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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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 / Iodide


Mass: 126.904 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: I
#6: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-3HY / 3-(hydroxymethyl)phenol


Mass: 124.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.36 Å3/Da / Density % sol: 47.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 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: 1.98→80.36 Å / Num. all: 41800 / Num. obs: 41862 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.0743 / Net I/σ(I): 3.5
Reflection shellResolution: 1.98→2.05 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.1646 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GC1

3gc1


Resolution: 1.98→54.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.991 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.21 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23754 2148 5 %RANDOM
Rwork0.19166 ---
obs0.19402 40586 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-1.19 Å2
2---0.08 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.98→54.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 153 504 5414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195052
X-RAY DIFFRACTIONr_bond_other_d0.0020.024733
X-RAY DIFFRACTIONr_angle_refined_deg1.771.9886870
X-RAY DIFFRACTIONr_angle_other_deg0.8883.00310868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9895592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97423.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03715804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8281538
X-RAY DIFFRACTIONr_chiral_restr0.0880.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215677
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021207
X-RAY DIFFRACTIONr_mcbond_it1.1291.9142378
X-RAY DIFFRACTIONr_mcbond_other1.1251.9132376
X-RAY DIFFRACTIONr_mcangle_it1.9352.8632966
X-RAY DIFFRACTIONr_mcangle_other1.9352.8632967
X-RAY DIFFRACTIONr_scbond_it1.3042.1292674
X-RAY DIFFRACTIONr_scbond_other1.3042.132675
X-RAY DIFFRACTIONr_scangle_other2.0073.1463905
X-RAY DIFFRACTIONr_long_range_B_refined7.18317.3386373
X-RAY DIFFRACTIONr_long_range_B_other7.18317.346374
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 165 -
Rwork0.215 3031 -
obs--99.59 %
Refinement TLS params.Method: refined / Origin x: 7.6127 Å / Origin y: -0.4449 Å / Origin z: 22.0729 Å
111213212223313233
T0.0161 Å2-0.0092 Å2-0.0199 Å2-0.0267 Å20.0176 Å2--0.0408 Å2
L1.5657 °20.3729 °20.4179 °2-2.7684 °2-0.6313 °2--1.7216 °2
S-0.01 Å °0.0468 Å °0.0387 Å °-0.1837 Å °0.1206 Å °0.3281 Å °0.0488 Å °-0.1871 Å °-0.1106 Å °

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