[English] 日本語
Yorodumi
- PDB-4okr: Structures of Toxoplasma gondii MIC2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4okr
TitleStructures of Toxoplasma gondii MIC2
ComponentsMicronemal protein MIC2
KeywordsCELL ADHESION / VWA domain / integrin I domain / TSR domain / Adhesin / gliding motility / cell surface
Function / homology
Function and homology information


: / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
alpha-D-mannopyranose / Micronemal protein MIC2
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsSong, G. / Springer, T.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structures of the Toxoplasma gliding motility adhesin.
Authors: Song, G. / Springer, T.A.
History
DepositionJan 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Micronemal protein MIC2
B: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4374
Polymers60,0762
Non-polymers3602
Water1,04558
1
A: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2182
Polymers30,0381
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Micronemal protein MIC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2182
Polymers30,0381
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.791, 148.052, 41.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein Micronemal protein MIC2 / Microneme protein MIC2


Mass: 30038.109 Da / Num. of mol.: 2 / Fragment: MIC2 (unp residues 67-337) / Mutation: S158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: TGVEG_201780 / Cell line (production host): HEK293T / Production host: homo sapiens (human) / References: UniProt: O00816
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.1 M sodium acetate, 0.2 M (NH4)2SO4, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 30, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→43.3 Å / Num. all: 15742 / Num. obs: 15634 / % possible obs: 99.3 % / Observed criterion σ(F): 100 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.268
Reflection shellResolution: 2.6→2.64 Å / % possible all: 63.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_1565)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→43.3 Å / SU ML: 0.41 / σ(F): 1.33 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2755 783 5.01 %
Rwork0.23 --
obs0.2323 15634 92.23 %
all-15742 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.601→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 22 58 3648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033674
X-RAY DIFFRACTIONf_angle_d0.7344994
X-RAY DIFFRACTIONf_dihedral_angle_d14.6271367
X-RAY DIFFRACTIONf_chiral_restr0.029578
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.76410.3819950.3171813X-RAY DIFFRACTION70
2.7641-2.97750.3291200.28852264X-RAY DIFFRACTION86
2.9775-3.2770.33381350.26482567X-RAY DIFFRACTION97
3.277-3.7510.30831410.22172682X-RAY DIFFRACTION100
3.751-4.72490.21691410.19272683X-RAY DIFFRACTION100
4.7249-43.40150.261510.2252842X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.7955 Å / Origin y: 34.9748 Å / Origin z: 9.8997 Å
111213212223313233
T0.2473 Å2-0.004 Å2-0.0663 Å2-0.3085 Å2-0.0232 Å2--0.2918 Å2
L0.7551 °21.0883 °2-0.773 °2-1.6577 °2-0.9272 °2--1.2401 °2
S-0.0439 Å °0.1213 Å °0.0574 Å °-0.0722 Å °0.0821 Å °0.0831 Å °0.0383 Å °-0.1049 Å °-0.0401 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