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- PDB-6m7e: Structure of bovine lactoperoxidase with multiple iodide ions in ... -

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Basic information

Entry
Database: PDB / ID: 6m7e
TitleStructure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxide family
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 / 1-(OXIDOSULFANYL)METHANAMINE / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsMaurya, A. / Viswanathan, V. / Pandey, N. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Structure of bovine lactoperoxidase with multiple iodide ions in the distaline heme cavity.
Authors: Maurya, A. / Viswanathan, V. / Pandey, N. / Singh, A.K. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMar 18, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 15, 2020ID: 4GN6
Revision 1.0Apr 15, 2020Provider: 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.pdbx_value_order / _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 2.1May 4, 2022Group: Database references / Structure summary / Category: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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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)71,98730
Polymers67,7731
Non-polymers4,21429
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-15 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.810, 80.673, 74.442
Angle α, β, γ (deg.)90.000, 103.070, 90.000
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 / / LPO


Mass: 67773.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P80025, 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
#5: 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 / 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 , 8 types, 214 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5NOS / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Ammonium Iodide, PEG 3350, pH 6.8, VAPOR DIFFUSION, HANGING DROP,

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.42→43.99 Å / Num. obs: 22380 / % possible obs: 93.8 % / Redundancy: 4.3 % / Rsym value: 0.114 / Net I/σ(I): 3.4
Reflection shellResolution: 2.42→2.48 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1766 / Rsym value: 0.314 / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GN6

4gn6
PDB Unreleased entry


Resolution: 2.42→43.953 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.179 / SU B: 11.362 / SU ML: 0.253 / Average fsc free: 0.872 / Average fsc work: 0.9073 / Cross valid method: FREE R-VALUE / ESU R: 1.19 / ESU R Free: 0.332
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2687 1146 5.121 %
Rwork0.1836 21234 -
all0.188 --
obs-22380 94.053 %
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: 57.688 Å2
Baniso -1Baniso -2Baniso -3
1--0.257 Å20 Å2-0.1 Å2
2---0.025 Å2-0 Å2
3---0.297 Å2
Refinement stepCycle: LAST / Resolution: 2.42→43.953 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 0 153 189 5113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135052
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174578
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6846868
X-RAY DIFFRACTIONr_angle_other_deg1.1921.60210644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8145596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48621.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52515826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6041538
X-RAY DIFFRACTIONr_chiral_restr0.0630.2630
X-RAY DIFFRACTIONr_chiral_restr_other0.0670.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025630
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021101
X-RAY DIFFRACTIONr_nbd_refined0.2110.21182
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.24572
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22333
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22091
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2187
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0520.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1260.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.220
X-RAY DIFFRACTIONr_nbd_other0.2340.271
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.213
X-RAY DIFFRACTIONr_mcbond_it4.0316.0752386
X-RAY DIFFRACTIONr_mcbond_other4.0326.0722380
X-RAY DIFFRACTIONr_mcangle_it6.0979.1022976
X-RAY DIFFRACTIONr_mcangle_other6.0869.1072976
X-RAY DIFFRACTIONr_scbond_it4.1746.3742666
X-RAY DIFFRACTIONr_scbond_other4.1736.3742666
X-RAY DIFFRACTIONr_scangle_it6.2679.4443891
X-RAY DIFFRACTIONr_scangle_other6.2679.4443891
X-RAY DIFFRACTIONr_lrange_it11.264111.33722977
X-RAY DIFFRACTIONr_lrange_other11.257111.36522923
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
2.42-2.4830.432670.26412000.27317600.6960.80271.98860.215
2.483-2.550.32760.23213170.23716900.8250.85182.4260.184
2.55-2.6240.368660.23713920.24316540.7970.85488.14990.188
2.624-2.7040.334590.21314690.21816130.8520.89494.73030.169
2.704-2.7930.335770.20914320.21515550.8570.90197.04180.171
2.793-2.890.306880.19913970.20515080.8550.90598.47480.163
2.89-2.9990.349740.21113790.21814620.8560.89399.38440.184
2.999-3.1210.369660.21713260.22414000.8330.89899.42860.19
3.121-3.2590.299750.21212460.21713320.8670.999.17420.19
3.259-3.4170.29510.19512350.212970.9020.92299.15190.182
3.417-3.6010.305610.18911610.19412370.8830.92898.78740.183
3.601-3.8170.258620.16910590.17411510.9180.94197.39360.165
3.817-4.0790.21510.1559970.15810930.9480.95595.88290.154
4.079-4.4030.224610.149260.14510250.9440.9696.29270.145
4.403-4.8180.238480.1558450.1599410.9460.95694.8990.167
4.818-5.3780.262350.1647970.1698620.9570.95996.51970.18
5.378-6.1950.246400.186910.1847450.9320.94898.12080.199
6.195-7.550.257380.1726120.1786520.9290.94599.69330.193
7.55-10.5230.215320.1614740.1645070.9470.96499.80280.189
10.523-43.9530.199190.2182790.2173050.9450.95497.70490.261

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