[English] 日本語
Yorodumi
- PDB-6bxw: Crystal structure of Toxoplasma gondii Mitochondrial Association ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bxw
TitleCrystal structure of Toxoplasma gondii Mitochondrial Association Factor 1 B (MAF1B) in complex with ADPribose
ComponentsMitochondrial association factor 1
KeywordsMEMBRANE PROTEIN / macro domain / ADPribose / neofuntionality
Function / homologysymbiont-containing vacuole membrane / cytoplasmic vesicle membrane / ADENOSINE-5-DIPHOSPHORIBOSE / Mitochondrial association factor 1 form b1
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsParker, M.L. / Ramaswamy, R. / Boulanger, M.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Discovery grant Canada
CitationJournal: Mol. Microbiol. / Year: 2018
Title: A Toxoplasma gondii locus required for the direct manipulation of host mitochondria has maintained multiple ancestral functions.
Authors: Blank, M.L. / Parker, M.L. / Ramaswamy, R. / Powell, C.J. / English, E.D. / Adomako-Ankomah, Y. / Pernas, L.F. / Workman, S.D. / Boothroyd, J.C. / Boulanger, M.J. / Boyle, J.P.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0462
Polymers29,4871
Non-polymers5591
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.470, 62.360, 89.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mitochondrial association factor 1


Mass: 29487.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: MAF1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140H546
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M ammonium sulfate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2012 / Details: Flat Si Rh coated M0
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→40.556 Å / Num. obs: 29065 / % possible obs: 93.4 % / Redundancy: 3.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.094 / Net I/σ(I): 7.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.2 / % possible all: 97.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BXR

6bxr


Resolution: 1.65→40.556 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.75
RfactorNum. reflection% reflection
Rfree0.2191 1447 4.99 %
Rwork0.1957 --
obs0.1969 29022 92.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.62 Å2 / Biso mean: 22.7313 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.65→40.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 36 105 2153
Biso mean--33.41 28.41 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042099
X-RAY DIFFRACTIONf_angle_d0.8562862
X-RAY DIFFRACTIONf_chiral_restr0.03317
X-RAY DIFFRACTIONf_plane_restr0.004373
X-RAY DIFFRACTIONf_dihedral_angle_d12.186747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.7090.25331340.21912846298097
1.709-1.77740.24731430.2232785292895
1.7774-1.85830.251540.21852754290894
1.8583-1.95630.23681410.2142785292694
1.9563-2.07880.23281420.20322797293994
2.0788-2.23930.22011370.19172718285592
2.2393-2.46470.2171610.19092750291193
2.4647-2.82120.22261510.19842708285991
2.8212-3.55410.22671530.19332735288891
3.5541-40.56820.18791310.18222697282885

+
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