[English] 日本語
Yorodumi
- PDB-8j67: Crystal structure of Toxoplasma gondii M2AP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j67
TitleCrystal structure of Toxoplasma gondii M2AP
ComponentsMIC2-associated protein
KeywordsCELL INVASION / Toxoplasma gondii / MIC2 / M2AP / TSR6 domain / structural biology
Function / homology: / MIC2-associated protein, central beta-domain / MIC2-associated protein
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsWang, F.F. / Zhang, D.J. / Zhang, S. / Springer, T.A. / Song, G.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171215 China
CitationJournal: Commun Biol / Year: 2023
Title: Structural insights into MIC2 recognition by MIC2-associated protein in Toxoplasma gondii.
Authors: Zhang, S. / Wang, F. / Zhang, D. / Liu, D. / Ding, W. / Springer, T.A. / Song, G.
History
DepositionApr 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MIC2-associated protein
B: MIC2-associated protein
C: MIC2-associated protein


Theoretical massNumber of molelcules
Total (without water)59,0583
Polymers59,0583
Non-polymers00
Water7,692427
1
A: MIC2-associated protein


Theoretical massNumber of molelcules
Total (without water)19,6861
Polymers19,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MIC2-associated protein


Theoretical massNumber of molelcules
Total (without water)19,6861
Polymers19,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MIC2-associated protein


Theoretical massNumber of molelcules
Total (without water)19,6861
Polymers19,6861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.588, 183.389, 84.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein MIC2-associated protein / MIC2-associated protein M2AP


Mass: 19685.992 Da / Num. of mol.: 3 / Mutation: N127R, S177N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGRH88_039670 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 / References: UniProt: Q967S9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes sodium pH 6.5, 1.35 M sodium citrate tribasic dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.81→45.85 Å / Num. obs: 59267 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.21 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Χ2: 1.02 / Net I/σ(I): 17.4
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.34 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3430 / CC1/2: 1 / Χ2: 0.99 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.81→45.85 Å / SU ML: 0.2307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 2939 4.96 %
Rwork0.1818 56286 -
obs0.1834 59225 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.57 Å2
Refinement stepCycle: LAST / Resolution: 1.81→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 0 427 4427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114095
X-RAY DIFFRACTIONf_angle_d1.19485557
X-RAY DIFFRACTIONf_chiral_restr0.0811639
X-RAY DIFFRACTIONf_plane_restr0.0098729
X-RAY DIFFRACTIONf_dihedral_angle_d6.7668559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.840.36851260.33862639X-RAY DIFFRACTION98.61
1.84-1.870.32951410.29342618X-RAY DIFFRACTION99.89
1.87-1.90.28941510.2612653X-RAY DIFFRACTION99.93
1.9-1.940.24811420.24122646X-RAY DIFFRACTION99.93
1.94-1.980.28351430.23212652X-RAY DIFFRACTION99.93
1.98-2.020.29171460.22542651X-RAY DIFFRACTION99.86
2.02-2.070.29951350.22182643X-RAY DIFFRACTION100
2.07-2.120.26841250.2132707X-RAY DIFFRACTION99.89
2.12-2.180.23751410.20022638X-RAY DIFFRACTION100
2.18-2.240.23281440.19662664X-RAY DIFFRACTION100
2.24-2.310.2211450.19052651X-RAY DIFFRACTION100
2.31-2.40.23271480.19932666X-RAY DIFFRACTION100
2.4-2.490.25491250.20892689X-RAY DIFFRACTION100
2.49-2.610.25721400.20432663X-RAY DIFFRACTION100
2.61-2.740.24951490.21522703X-RAY DIFFRACTION99.96
2.74-2.920.24791550.20692659X-RAY DIFFRACTION99.96
2.92-3.140.20721550.20092693X-RAY DIFFRACTION99.93
3.14-3.460.17831380.16752696X-RAY DIFFRACTION99.93
3.46-3.960.18811150.15032749X-RAY DIFFRACTION99.93
3.96-4.980.17321310.13682747X-RAY DIFFRACTION99.83
4.98-45.850.1881440.16922859X-RAY DIFFRACTION99.57
Refinement TLS params.Method: refined / Origin x: 64.1570422243 Å / Origin y: 68.3709853889 Å / Origin z: 24.0934205063 Å
111213212223313233
T0.223685206672 Å2-0.00995016231874 Å2-0.00201874957862 Å2-0.223128439772 Å2-0.00294148232285 Å2--0.203847964317 Å2
L0.856830536712 °2-0.265903730558 °2-0.18582296367 °2-0.399687697879 °20.0519725217115 °2--0.66600214577 °2
S0.0134874149179 Å °0.11684284358 Å °-0.117180134533 Å °-0.00319551544521 Å °-0.0243018717105 Å °-0.0233027516055 Å °0.0151558919786 Å °-0.033016447045 Å °0.0166369917013 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