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- PDB-6yir: Crystal structure of Bacillus subtilis MsmX ATPase -

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Basic information

Entry
Database: PDB / ID: 6yir
TitleCrystal structure of Bacillus subtilis MsmX ATPase
ComponentsOligosaccharides import ATP-binding protein MsmX
KeywordsHYDROLASE / ATPase / Polysaccharide import / Multitask
Function / homology
Function and homology information


Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate / polysaccharide transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATPase-coupled transmembrane transporter activity / hydrolase activity / ATP binding
Similarity search - Function
Transport-associated OB, type 1 / TOBE domain / MalK, OB fold domain / MalK OB fold domain / Molybdate/tungstate binding, C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Transport-associated OB, type 1 / TOBE domain / MalK, OB fold domain / MalK OB fold domain / Molybdate/tungstate binding, C-terminal / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Oligosaccharides import ATP-binding protein MsmX
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsLeisico, F. / Santos-Silva, T. / Romao, M.J.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BIA-MIC/30696/2017 Portugal
CitationJournal: Sci Rep / Year: 2020
Title: Multitask ATPases (NBDs) of bacterial ABC importers type I and their interspecies exchangeability.
Authors: Leisico, F. / Godinho, L.M. / Goncalves, I.C. / Silva, S.P. / Carneiro, B. / Romao, M.J. / Santos-Silva, T. / de Sa-Nogueira, I.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oligosaccharides import ATP-binding protein MsmX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6863
Polymers42,4401
Non-polymers2462
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-13 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.758, 94.247, 132.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Oligosaccharides import ATP-binding protein MsmX / Maltodextrin import ATP-binding protein MsmX / Melibiose/raffinose/stachyose import ATP-binding protein MsmX


Mass: 42439.988 Da / Num. of mol.: 1 / Mutation: K43A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: msmX, yxkG, BSU38810 / Production host: Escherichia coli (E. coli)
References: UniProt: P94360, Translocases; Catalysing the translocation of carbohydrates and their derivatives; Linked to the hydrolysis of a nucleoside triphosphate
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM ammonium sulfate, 100 mM HEPES pH 7.5 and 30% (w/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9919 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.67→45.93 Å / Num. obs: 41647 / % possible obs: 95 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 18
Reflection shellResolution: 1.67→1.8 Å / Num. unique obs: 2082 / CC1/2: 0.518

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
STARANISOdata scaling
Aimlessdata scaling
ARP/wARPmodel building
Cootmodel building
PHASERphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V43, 1Q12

1v43

1q12


Resolution: 1.68→19.97 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.926 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.143
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 2135 5.3 %RANDOM
Rwork0.197 ---
obs0.1997 38380 65.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.84 Å2 / Biso mean: 42.441 Å2 / Biso min: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.68→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2912 0 15 257 3184
Biso mean--61.78 49.7 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193032
X-RAY DIFFRACTIONr_bond_other_d0.0020.023021
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9754083
X-RAY DIFFRACTIONr_angle_other_deg1.03236959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8875379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9923.944142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1215580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5541524
X-RAY DIFFRACTIONr_chiral_restr0.1290.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023389
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02679
LS refinement shellResolution: 1.68→1.722 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.275 9 -
Rwork0.305 94 -
obs--2.3 %

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