[English] 日本語
Yorodumi
- PDB-6lf7: Crystal structure of the complex of goat lactoperoxidase with hyp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lf7
TitleCrystal structure of the complex of goat lactoperoxidase with hypothiocyanite and hydrogen peroxide at 1.79 A resolution.
ComponentsLactoperoxidase
KeywordsOXIDOREDUCTASE / Peroxide family
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 / hydrogen peroxide catabolic process / peroxidase activity / 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 / hydrogen peroxide catabolic process / peroxidase activity / 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
PROTOPORPHYRIN IX CONTAINING FE / IODIDE ION / 1-(OXIDOSULFANYL)METHANAMINE / HYDROGEN PEROXIDE / THIOCYANATE ION / Lactoperoxidase
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å
AuthorsViswanathan, V. / Tyagi, T.K. / Singh, R.P. / Singh, A.K. / Singh, A. / Bhushan, A. / Sinha, M. / Kaur, 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 the complex of goat lactoperoxidase with hypothiocyanite and hydrogen peroxide at 1.79 A resolution.
Authors: Viswanathan, V. / Tyagi, T.K. / Singh, R.P. / Singh, A.K. / Singh, A. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionNov 30, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 22, 2020ID: 4N7A
Revision 1.0Jan 22, 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_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 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_type / chem_comp ...atom_type / chem_comp / 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 / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactoperoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,82939
Polymers67,5721
Non-polymers4,25738
Water8,791488
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.881, 80.731, 75.139
Angle α, β, γ (deg.)90.000, 101.530, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 4 molecules A

#1: Protein Lactoperoxidase


Mass: 67571.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / References: UniProt: A0A452E9Y6, peroxidase
#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.: 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

-
Non-polymers , 9 types, 523 molecules

#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 126.904 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-OSM / 1-(OXIDOSULFANYL)METHANAMINE


Mass: 79.122 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CH5NOS / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.13 %
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

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 21, 2013 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.79→27.214 Å / Num. obs: 56910 / % possible obs: 96.38 % / Redundancy: 8.3 % / CC1/2: 0.94 / Rsym value: 0.099 / Net I/σ(I): 7.2
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 4329 / CC1/2: 0.89 / % possible all: 84.83

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N7A

4n7a
PDB Unreleased entry


Resolution: 1.794→27.214 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: FREE R-VALUE / ESU R: 0.176 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2966 2871 5.045 %
Rwork0.231 --
all0.234 --
obs-56910 96.382 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.996 Å2
Baniso -1Baniso -2Baniso -3
1--0.126 Å2-0 Å2-0.012 Å2
2--0.273 Å20 Å2
3----0.131 Å2
Refinement stepCycle: LAST / Resolution: 1.794→27.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 175 488 5420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135105
X-RAY DIFFRACTIONr_bond_other_d0.0340.0174652
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6756905
X-RAY DIFFRACTIONr_angle_other_deg3.051.60110798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9825610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91921.815281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78715830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5161539
X-RAY DIFFRACTIONr_chiral_restr0.0820.2626
X-RAY DIFFRACTIONr_chiral_restr_other2.9650.29
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025659
X-RAY DIFFRACTIONr_gen_planes_other0.0250.021106
X-RAY DIFFRACTIONr_nbd_refined0.2540.21274
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2320.24814
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22381
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.2396
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0430.23
X-RAY DIFFRACTIONr_metal_ion_refined0.1430.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.218
X-RAY DIFFRACTIONr_nbd_other0.2980.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1890.219
X-RAY DIFFRACTIONr_mcbond_it2.8983.6132414
X-RAY DIFFRACTIONr_mcbond_other2.9033.6172397
X-RAY DIFFRACTIONr_mcangle_it4.4645.4213005
X-RAY DIFFRACTIONr_mcangle_other4.4545.4232997
X-RAY DIFFRACTIONr_scbond_it2.8083.8592691
X-RAY DIFFRACTIONr_scbond_other2.8073.8592692
X-RAY DIFFRACTIONr_scangle_it4.3455.7183892
X-RAY DIFFRACTIONr_scangle_other4.3445.7183893
X-RAY DIFFRACTIONr_lrange_it8.20942.8746090
X-RAY DIFFRACTIONr_lrange_other8.15142.6295989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.794-1.840.3891670.3113473X-RAY DIFFRACTION84.0841
1.84-1.8910.392080.3543915X-RAY DIFFRACTION98.2134
1.891-1.9450.6411860.6423412X-RAY DIFFRACTION87.0765
1.945-2.0050.4112160.3053744X-RAY DIFFRACTION98.7777
2.005-2.0710.2911890.2453722X-RAY DIFFRACTION99.7195
2.071-2.1440.3041620.2363554X-RAY DIFFRACTION99.7316
2.144-2.2240.3161770.3043275X-RAY DIFFRACTION95.3591
2.224-2.3150.4731660.4323116X-RAY DIFFRACTION93.611
2.315-2.4180.2951720.2183174X-RAY DIFFRACTION99.8806
2.418-2.5360.321770.2023016X-RAY DIFFRACTION99.7812
2.536-2.6730.2631510.1922884X-RAY DIFFRACTION99.7371
2.673-2.8350.2751550.212736X-RAY DIFFRACTION99.7929
2.835-3.030.2861430.1972580X-RAY DIFFRACTION99.8533
3.03-3.2720.2541340.1942375X-RAY DIFFRACTION99.6822
3.272-3.5840.231080.182225X-RAY DIFFRACTION99.15
3.584-4.0060.231980.1641906X-RAY DIFFRACTION95.8393
4.006-4.6230.1911000.1481765X-RAY DIFFRACTION98.2096
4.623-5.6570.248730.161482X-RAY DIFFRACTION98.8557
5.657-7.9760.25640.1781174X-RAY DIFFRACTION99.5177
7.976-27.210.308250.197511X-RAY DIFFRACTION75.493

+
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://pdbjlvh1.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