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- PDB-6t84: crystal structure of the mycobacterial trehalose monomycolate tra... -

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Basic information

Entry
Database: PDB / ID: 6t84
Titlecrystal structure of the mycobacterial trehalose monomycolate transport factor A, TtfA
ComponentsUncharacterized protein
KeywordsLIPID TRANSPORT / trehalose monomycolate / MmpL3 accessory protein
Function / homology: / : / cell tip / cell septum / lipid transport / cell wall organization / plasma membrane / Trehalose monomycolate transport factor A
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsBlaise, M.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0008-01 France
CitationJournal: Proteins / Year: 2020
Title: The crystal structure of the mycobacterial trehalose monomycolate transport factor A, TtfA, reveals an atypical fold.
Authors: Ung, K.L. / Alsarraf, H.M.A.B. / Kremer, L. / Blaise, M.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6103
Polymers21,4181
Non-polymers1922
Water3,297183
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-22 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.240, 70.090, 86.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 21417.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GHM in N-terminus is a tag as well as AS in C-terminus
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_0736 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0QQF4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 28% PEG 4000 and 0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.4→46.54 Å / Num. obs: 37320 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 17.93 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05072 / Rpim(I) all: 0.02624 / Rrim(I) all: 0.05729 / Net I/σ(I): 14.79
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 1.118 / Num. unique obs: 3670 / CC1/2: 0.589

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→46.54 Å / SU ML: 0.1644 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8485
RfactorNum. reflection% reflection
Rfree0.1985 1865 5 %
Rwork0.1739 --
obs0.1751 37306 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.14 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 0 10 183 1628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01291592
X-RAY DIFFRACTIONf_angle_d1.23312176
X-RAY DIFFRACTIONf_chiral_restr0.1096234
X-RAY DIFFRACTIONf_plane_restr0.0074287
X-RAY DIFFRACTIONf_dihedral_angle_d12.9884614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.31241410.29462685X-RAY DIFFRACTION99.44
1.44-1.480.31421420.26432694X-RAY DIFFRACTION99.65
1.48-1.530.26551420.23662691X-RAY DIFFRACTION99.75
1.53-1.580.23811410.20122681X-RAY DIFFRACTION99.82
1.58-1.650.22121410.18692695X-RAY DIFFRACTION99.75
1.65-1.720.20351430.17742730X-RAY DIFFRACTION99.79
1.72-1.810.20731430.16592704X-RAY DIFFRACTION99.72
1.81-1.920.20591420.16352704X-RAY DIFFRACTION99.82
1.92-2.070.19031430.15562715X-RAY DIFFRACTION99.69
2.07-2.280.20111440.15742738X-RAY DIFFRACTION100
2.28-2.610.19941450.18152752X-RAY DIFFRACTION99.97
2.61-3.290.20541460.1772766X-RAY DIFFRACTION99.93
3.29-46.540.16771520.1612886X-RAY DIFFRACTION99.57

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