[English] 日本語
Yorodumi
- PDB-5ouq: Structure of TgPLP1 MACPF domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ouq
TitleStructure of TgPLP1 MACPF domain
ComponentsPerforin-like protein 1
KeywordsLIPID BINDING PROTEIN / Toxoplasma / cell egress / MACPF domain
Function / homology
Function and homology information


microneme membrane / exit from host cell / symbiont-containing vacuole membrane / wide pore channel activity / cytoplasmic vesicle / killing of cells of another organism
Similarity search - Function
membrane-attack complex / perforin / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain
Similarity search - Domain/homology
Perforin-like protein 1 / Perforin-like protein 1
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.11 Å
AuthorsNi, T. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000331/1 United Kingdom
CitationJournal: Sci Adv / Year: 2018
Title: Structures of monomeric and oligomeric forms of theToxoplasma gondiiperforin-like protein 1.
Authors: Ni, T. / Williams, S.I. / Rezelj, S. / Anderluh, G. / Harlos, K. / Stansfeld, P.J. / Gilbert, R.J.C.
History
DepositionAug 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _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: Perforin-like protein 1
C: Perforin-like protein 1
D: Perforin-like protein 1
E: Perforin-like protein 1
F: Perforin-like protein 1
G: Perforin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,00412
Polymers234,6766
Non-polymers1,3276
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-4 kcal/mol
Surface area74750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.490, 185.740, 104.190
Angle α, β, γ (deg.)90.00, 121.48, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Perforin-like protein 1


Mass: 39112.723 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: PLP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: G3G7T1, UniProt: V5BCL0*PLUS
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES pH7.5, 10% alcohol mixture, 15% PEG 1000, 15% PEG 3350, 15% MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 5.11→56.35 Å / Num. obs: 10514 / % possible obs: 99.7 % / Redundancy: 6.7 % / Net I/σ(I): 8.2

-
Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OUP

5oup


Resolution: 5.11→56.35 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 40.47
RfactorNum. reflection% reflection
Rfree0.2979 499 4.75 %
Rwork0.2867 --
obs0.2872 10497 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 5.11→56.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12864 0 84 0 12948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313260
X-RAY DIFFRACTIONf_angle_d0.63818018
X-RAY DIFFRACTIONf_dihedral_angle_d16.1437920
X-RAY DIFFRACTIONf_chiral_restr0.0441968
X-RAY DIFFRACTIONf_plane_restr0.0052364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.11-5.6240.34841170.3532500X-RAY DIFFRACTION99
5.624-6.43730.33891360.31292483X-RAY DIFFRACTION100
6.4373-8.10820.31461270.31242494X-RAY DIFFRACTION100
8.1082-68.01430.27411190.2612521X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -14.2163 Å / Origin y: -54.7316 Å / Origin z: 13.0183 Å
111213212223313233
T2.4754 Å20.1245 Å20.5722 Å2-2.9938 Å2-0.1126 Å2--2.1058 Å2
L1.8147 °20.3748 °20.3052 °2-1.9624 °2-0.0931 °2--0.8277 °2
S-0.2737 Å °-0.5253 Å °-0.0931 Å °0.3988 Å °0.2132 Å °0.3221 Å °0.2156 Å °-0.4151 Å °0 Å °
Refinement TLS groupSelection details: all

+
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