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- PDB-6bxs: Crystal structure of Toxoplasma gondii Mitochondrial Association ... -

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Basic information

Entry
Database: PDB / ID: 6bxs
TitleCrystal structure of Toxoplasma gondii Mitochondrial Association Factor 1 A (MAF1A)
Componentsmitochondrial association factor 1
KeywordsMEMBRANE PROTEIN / macro domain / ADPribose / neofunctionalize
Function / homologysymbiont-containing vacuole membrane / membrane / Mitochondrial association factor 1 form a1
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRamaswamy, 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 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mitochondrial association factor 1
B: mitochondrial association factor 1
C: mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,91817
Polymers92,5733
Non-polymers1,34514
Water2,864159
1
A: mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3386
Polymers30,8581
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2425
Polymers30,8581
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3386
Polymers30,8581
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.890, 49.670, 114.750
Angle α, β, γ (deg.)90.000, 96.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein mitochondrial association factor 1


Mass: 30857.760 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: MAF1 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): TGGT1_279100 / Variant (production host): ATCC 50853 / GT1 / References: UniProt: A0A193AUK9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.9 M ammonium sulfate, 0.1M Hepes pH 7.0, 0.5% PEG8000, 3% 2- methyl- 2,4- pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 27, 2014
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→48.86 Å / Num. obs: 51862 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 3 / % possible all: 92.4

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Phasing

PhasingMethod: molecular replacement

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Processing

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

6bxr


Resolution: 2.1→48.86 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.92
RfactorNum. reflection% reflection
Rfree0.2443 2650 5.11 %
Rwork0.2121 --
obs0.2138 51852 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 33.6138 Å2 / Biso min: 15.37 Å2
Refinement stepCycle: final / Resolution: 2.1→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6294 0 70 159 6523
Biso mean--47.79 31.46 -
Num. residues----812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036494
X-RAY DIFFRACTIONf_angle_d0.6868816
X-RAY DIFFRACTIONf_chiral_restr0.029953
X-RAY DIFFRACTIONf_plane_restr0.0021159
X-RAY DIFFRACTIONf_dihedral_angle_d13.3262374
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13820.33521280.26922331245989
2.1382-2.17930.25061300.26242539266998
2.1793-2.22380.27131440.24932563270798
2.2238-2.27220.28911280.22812604273298
2.2722-2.3250.241250.22462557268298
2.325-2.38310.28141340.22552575270999
2.3831-2.44760.2281330.22492607274098
2.4476-2.51960.25541250.23092572269798
2.5196-2.60090.27161530.23342603275698
2.6009-2.69390.27311270.23792568269599
2.6939-2.80170.30341470.23782586273399
2.8017-2.92920.2791650.24262607277299
2.9292-3.08360.30571380.2482591272999
3.0836-3.27680.251470.23042606275399
3.2768-3.52970.24791450.21782617276299
3.5297-3.88480.23591580.18662597275599
3.8848-4.44660.18751480.16422662281099
4.4466-5.6010.1921320.16662660279299
5.601-48.8730.21951430.20292757290099

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