[English] 日本語
Yorodumi
- PDB-7d52: Crystal structure of yak lactoperoxidase with a disordered propio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d52
TitleCrystal structure of yak lactoperoxidase with a disordered propionic group of heme moiety at 2.20 A resolution
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Lactoperoxidase
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
: / Haem peroxidase, animal-type / Haem peroxidase domain superfamily, animal type / Animal haem peroxidase / Animal heme peroxidase superfamily profile. / Haem peroxidase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Lactoperoxidase
Similarity search - Component
Biological speciesBos mutus (wild yak)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSingh, P.K. / 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
DepositionSep 24, 2020Deposition site: PDBJ / Processing site: PDBJ
SupersessionOct 14, 2020ID: 6L4F
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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 1.2Apr 21, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,72311
Polymers67,7731
Non-polymers1,95010
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-64 kcal/mol
Surface area24690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.980, 85.080, 98.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 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, peroxidase

-
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-ROHGlycam 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
[][D-1-deoxy-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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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

-
Non-polymers , 6 types, 456 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.2M potassium fluoride, 20% PEG 3350 / PH range: 5-8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / 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: 2.2→85 Å / Num. obs: 35006 / % possible obs: 100 % / Redundancy: 12 % / CC1/2: 0.993 / Rsym value: 0.2 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 11 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2333 / CC1/2: 0.967 / Rsym value: 0.99 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BXI

3bxi


Resolution: 2.2→62.274 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.89 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.161 / SU B: 7.548 / SU ML: 0.179 / Average fsc free: 0.8708 / Average fsc work: 0.8918 / Cross valid method: FREE R-VALUE / ESU R: 0.29 / ESU R Free: 0.226
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2498 1806 5.198 %
Rwork0.1902 32941 -
all0.193 --
obs-34747 99.416 %
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: 28.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.031 Å20 Å2-0 Å2
2---0.041 Å20 Å2
3---0.011 Å2
Refinement stepCycle: LAST / Resolution: 2.2→62.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 118 450 5338
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0125037
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6776855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1615594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99721.841277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.30915825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8941538
X-RAY DIFFRACTIONr_chiral_restr0.1140.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023899
X-RAY DIFFRACTIONr_nbd_refined0.2240.22519
X-RAY DIFFRACTIONr_nbtor_refined0.3140.23416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2442
X-RAY DIFFRACTIONr_metal_ion_refined0.3210.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2010.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2660.28
X-RAY DIFFRACTIONr_mcbond_it2.4122.7252379
X-RAY DIFFRACTIONr_mcangle_it3.994.0742972
X-RAY DIFFRACTIONr_scbond_it2.832.9172658
X-RAY DIFFRACTIONr_scangle_it4.3854.293883
X-RAY DIFFRACTIONr_lrange_it8.50549.77222579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.4151360.4152333X-RAY DIFFRACTION97.243
2.257-2.3190.3291020.2912312X-RAY DIFFRACTION96.7535
2.319-2.3860.2971340.2212253X-RAY DIFFRACTION99.8745
2.386-2.4590.2811300.2142218X-RAY DIFFRACTION99.9149
2.459-2.540.2731340.2022152X-RAY DIFFRACTION99.9126
2.54-2.6290.2681100.22073X-RAY DIFFRACTION99.8628
2.629-2.7280.3131050.2252037X-RAY DIFFRACTION99.7207
2.728-2.8390.3151170.1841945X-RAY DIFFRACTION99.9515
2.839-2.9650.2651020.1751850X-RAY DIFFRACTION99.7955
2.965-3.110.249920.1781807X-RAY DIFFRACTION100
3.11-3.2770.215860.1661716X-RAY DIFFRACTION99.9445
3.277-3.4760.227810.1761616X-RAY DIFFRACTION99.5308
3.476-3.7150.202870.1641524X-RAY DIFFRACTION99.6289
3.715-4.0110.223640.1681436X-RAY DIFFRACTION99.3378
4.011-4.3920.239650.1391328X-RAY DIFFRACTION100
4.392-4.9080.165800.131182X-RAY DIFFRACTION99.9208
4.908-5.6620.225710.1461066X-RAY DIFFRACTION100
5.662-6.9210.237490.169917X-RAY DIFFRACTION100
6.921-9.7320.168480.136724X-RAY DIFFRACTION100
8-100.297130.191452X-RAY DIFFRACTION98.9362

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more