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- PDB-7c75: Crystal structure of yak lactoperoxidase with partially coordinat... -

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Basic information

Entry
Database: PDB / ID: 7c75
TitleCrystal structure of yak lactoperoxidase with partially coordinated Na ion in the distal heme cavity
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase
Function / homology
Function and homology information


thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane / heme binding / calcium ion binding ...thiocyanate peroxidase activity / detection of chemical stimulus involved in sensory perception of bitter taste / peroxidase / lactoperoxidase activity / hydrogen peroxide catabolic process / antibacterial humoral response / response to oxidative stress / basolateral plasma membrane / heme binding / calcium ion 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 / : / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSingh, P.K. / Viswanathan, V. / Rani, C. / Ahmad, N. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2021
Title: Potassium-induced partial inhibition of lactoperoxidase: structure of the complex of lactoperoxidase with potassium ion at 2.20 angstrom resolution.
Authors: Singh, P.K. / Pandey, S. / Rani, C. / Ahmad, N. / Viswanathan, V. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 22, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 24, 2020ID: 6L3Z
Revision 1.0Jun 24, 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 / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _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_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_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 3, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)69,44210
Polymers67,7731
Non-polymers1,6699
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-34 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.910, 84.830, 98.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Lactoperoxidase


Mass: 67773.305 Da / Num. of mol.: 1 / 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


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 , 6 types, 399 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M Sodium Fluoride, 20% PEG 3350 / PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 19, 2019 / Details: mirror
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→64.3 Å / Num. obs: 18790 / % possible obs: 99.3 % / Redundancy: 9.9 % / CC1/2: 0.97 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1265 / CC1/2: 0.83 / Rpim(I) all: 0.34 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L3Z

6l3z
PDB Unreleased entry


Resolution: 2.7→64.295 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.829 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.179 / SU B: 15.846 / SU ML: 0.311 / Average fsc free: 0.878 / Average fsc work: 0.9093 / Cross valid method: FREE R-VALUE / ESU R Free: 0.4
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2675 893 4.753 %
Rwork0.193 17896 -
all0.197 --
obs-18789 98.931 %
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: 25.515 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å2-0 Å2-0 Å2
2--0.172 Å2-0 Å2
3----0.233 Å2
Refinement stepCycle: LAST / Resolution: 2.7→64.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4784 0 89 395 5268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135044
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174560
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.6846854
X-RAY DIFFRACTIONr_angle_other_deg1.1921.59910600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1885594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90721.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10415825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1461538
X-RAY DIFFRACTIONr_chiral_restr0.0650.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025634
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021105
X-RAY DIFFRACTIONr_nbd_refined0.2140.21316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.24854
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22364
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2369
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1080.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.217
X-RAY DIFFRACTIONr_nbd_other0.2110.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3320.211
X-RAY DIFFRACTIONr_mcbond_it2.5852.742382
X-RAY DIFFRACTIONr_mcbond_other2.5492.7382381
X-RAY DIFFRACTIONr_mcangle_it4.4724.1032972
X-RAY DIFFRACTIONr_mcangle_other4.4764.1072973
X-RAY DIFFRACTIONr_scbond_it2.0972.7942660
X-RAY DIFFRACTIONr_scbond_other2.0982.7972655
X-RAY DIFFRACTIONr_scangle_it3.6754.1593880
X-RAY DIFFRACTIONr_scangle_other3.6744.1593880
X-RAY DIFFRACTIONr_lrange_it8.13431.1076082
X-RAY DIFFRACTIONr_lrange_other8.0731.1516013
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
2.7-2.770.332770.28512650.28813810.7560.80197.1760.26
2.77-2.8460.32670.26412400.26713420.8230.83497.3920.237
2.846-2.9280.287490.23512230.23713010.8120.8697.7710.208
2.928-3.0180.374640.22311920.2312760.7760.87498.43260.192
3.018-3.1170.326700.20311460.21112270.8740.89899.10350.178
3.117-3.2260.251490.20811410.2111970.8970.90399.41520.18
3.226-3.3470.32600.19210790.19911470.870.91199.30250.176
3.347-3.4840.226490.18410700.18611220.9260.93899.73260.169
3.484-3.6380.222280.16810500.1710820.9350.94999.63030.157
3.638-3.8150.246410.1799760.18210200.9250.94699.70590.174
3.815-4.0210.231500.1869240.1889790.910.93399.48930.18
4.021-4.2640.266380.1798840.1839250.8930.92999.67570.175
4.264-4.5570.245400.1728210.1758640.8950.94399.65280.173
4.557-4.920.283310.1557950.1598290.9420.9699.63810.151
4.92-5.3860.275530.1796960.1867560.9260.94699.07410.171
5.386-6.0160.254300.2096670.2126990.9330.93399.71390.199
6.016-6.9370.178350.1685800.1696180.9630.95499.51460.159
6.937-8.4710.217160.1265160.1285380.9610.97698.88480.128
8.471-11.8780.192320.1493870.1524230.9570.97199.05440.161
11.878-64.2950.238140.2472440.2472660.9560.94396.99250.3

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