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

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Basic information

Entry
Database: PDB / ID: 6bxt
TitleCrystal structure of Toxoplasma gondii Mitochondrial Association Factor 1 A (MAF1A) in complex with ADPribose
Componentsmitochondrial association factor 1
KeywordsMEMBRANE PROTEIN / macro domain / ADPribose / neofunctionalize
Function / homologysymbiont-containing vacuole membrane / membrane / ADENOSINE-5-DIPHOSPHORIBOSE / Mitochondrial association factor 1 form a1
Function and homology information
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 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

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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)93,6925
Polymers92,5733
Non-polymers1,1192
Water28816
1
A: mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4172
Polymers30,8581
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: mitochondrial association factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4172
Polymers30,8581
Non-polymers5591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: mitochondrial association factor 1


Theoretical massNumber of molelcules
Total (without water)30,8581
Polymers30,8581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.230, 49.520, 115.710
Angle α, β, γ (deg.)90.000, 96.630, 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) / References: UniProt: A0A193AUK9
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.9 M Ammonium sulfate, 0.1 M 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: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014 / Details: Rh coated flat
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→27.4 Å / Num. obs: 23134 / % possible obs: 94.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 50.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.2 / % possible all: 87.9

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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: 6BXS

6bxs


Resolution: 2.7→27.397 Å / SU ML: 0.46 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 33.62
RfactorNum. reflection% reflection
Rfree0.2856 1127 4.88 %
Rwork0.2326 --
obs0.2352 23084 93.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.35 Å2 / Biso mean: 60.8515 Å2 / Biso min: 26.59 Å2
Refinement stepCycle: final / Resolution: 2.7→27.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6001 0 72 16 6089
Biso mean--68.62 42.58 -
Num. residues----777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036213
X-RAY DIFFRACTIONf_angle_d0.6718445
X-RAY DIFFRACTIONf_chiral_restr0.028937
X-RAY DIFFRACTIONf_plane_restr0.0031101
X-RAY DIFFRACTIONf_dihedral_angle_d13.5332248
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.82280.39851240.34522489261386
2.8228-2.97140.40741460.31362757290396
2.9714-3.15730.35261510.27222853300498
3.1573-3.40070.31971490.26822810295997
3.4007-3.74220.32081360.22852830296697
3.7422-4.28190.25161290.20232554268387
4.2819-5.3880.21981490.19242883303298
5.388-27.39860.2671430.22262781292492

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