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- PDB-5xu1: Structure of a non-canonical ABC transporter from Streptococcus p... -

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Basic information

Entry
Database: PDB / ID: 5xu1
TitleStructure of a non-canonical ABC transporter from Streptococcus pneumoniae R6
Components
  • ABC transporter ATP-binding protein
  • ABC transporter permeae
KeywordsTRANSPORT PROTEIN / ABC transporter
Function / homology
Function and homology information


transmembrane transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...: / MacB-like periplasmic core domain / MacB-like periplasmic core domain / MacB, ATP-binding domain / ABC3 transporter permease protein domain / FtsX-like permease family / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ABC transporter permeae / ABC transporter domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsYang, H.B. / Jiang, Y.L. / Hou, W.T. / Chen, M.T. / Chen, Y. / Zhou, C.Z.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology2015CB910103 China
National Natural Science Foundation of China31400628 China
CitationJournal: Nat Commun / Year: 2018
Title: Structure of a MacAB-like efflux pump from Streptococcus pneumoniae.
Authors: Yang, H.B. / Hou, W.T. / Cheng, M.T. / Jiang, Y.L. / Chen, Y. / Zhou, C.Z.
History
DepositionJun 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 22, 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: ABC transporter ATP-binding protein
B: ABC transporter ATP-binding protein
M: ABC transporter permeae
S: ABC transporter permeae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,8636
Polymers144,8144
Non-polymers492
Water28816
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-66 kcal/mol
Surface area55210 Å2
Unit cell
Length a, b, c (Å)141.053, 154.987, 205.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ABC transporter ATP-binding protein


Mass: 27090.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: ABC-NBD, spr0694 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQF8
#2: Protein ABC transporter permeae / TMD of the ABC trasnporter


Mass: 45316.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6 / Gene: spr0695 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQF7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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: 3.89 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, 25-31% v/v PEG 550 MME, 0.01 M Cadmium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 34560 / % possible obs: 100 % / Redundancy: 13.5 % / Net I/σ(I): 13.3
Reflection shellResolution: 3.3→3.4 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3O

1f3o


Resolution: 3.3→50 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.871 / SU B: 26.417 / SU ML: 0.417 / Cross valid method: THROUGHOUT / ESU R Free: 0.517 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28922 1727 5 %RANDOM
Rwork0.23363 ---
obs0.23643 32666 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.664 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å2-0 Å2
2--2.22 Å20 Å2
3----4.66 Å2
Refinement stepCycle: 1 / Resolution: 3.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9269 0 2 16 9287
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199385
X-RAY DIFFRACTIONr_bond_other_d0.0020.029170
X-RAY DIFFRACTIONr_angle_refined_deg1.2981.98212668
X-RAY DIFFRACTIONr_angle_other_deg0.96321286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82751207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48725.257369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55151747
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4761545
X-RAY DIFFRACTIONr_chiral_restr0.0710.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021728
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3138.3284852
X-RAY DIFFRACTIONr_mcbond_other3.3138.3284851
X-RAY DIFFRACTIONr_mcangle_it5.54112.4866051
X-RAY DIFFRACTIONr_mcangle_other5.5412.4856052
X-RAY DIFFRACTIONr_scbond_it2.888.6284533
X-RAY DIFFRACTIONr_scbond_other2.8798.6284534
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.99812.8186618
X-RAY DIFFRACTIONr_long_range_B_refined8.25898.91610208
X-RAY DIFFRACTIONr_long_range_B_other8.25898.9210208
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.288→3.373 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 137 -
Rwork0.301 2302 -
obs--95.8 %

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