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- PDB-8b5e: Exploring the ligand binding and conformational dynamics of recep... -

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Basic information

Entry
Database: PDB / ID: 8b5e
TitleExploring the ligand binding and conformational dynamics of receptor domain 1 of the ABC transporter GlnPQ
ComponentsABC transporter permease subunit
KeywordsTRANSPORT PROTEIN / Transporter / membrane protein
Function / homology
Function and homology information


peptide transport / ligand-gated monoatomic ion channel activity / ATP-binding cassette (ABC) transporter complex / protein transport
Similarity search - Function
Amino acid ABC transporter, permease protein, 3-TM domain / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF ...Amino acid ABC transporter, permease protein, 3-TM domain / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins.
Similarity search - Domain/homology
ARGININE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamine transport system permease protein GlnP
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWhittaker, J. / Guskov, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Phys.Chem.B / Year: 2024
Title: Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ.
Authors: Nemchinova, M. / Schuurman-Wolters, G.K. / Whittaker, J.J. / Arkhipova, V. / Marrink, S.J. / Poolman, B. / Guskov, A.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter permease subunit
B: ABC transporter permease subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,18612
Polymers49,0392
Non-polymers1,14610
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint7 kcal/mol
Surface area19670 Å2
Unit cell
Length a, b, c (Å)34.670, 53.080, 54.080
Angle α, β, γ (deg.)92.400, 92.370, 94.110
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ABC transporter permease subunit / Glutamine transport system permease protein GlnP


Mass: 24519.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: glnP, AMHIJAGA_02474, GII02_01815 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) / References: UniProt: A0A2X0R690

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Non-polymers , 6 types, 271 molecules

#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM NaCl 50 mM TRIS 10 % MPD 15 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2020
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→53.98 Å / Num. obs: 50688 / % possible obs: 99 % / Redundancy: 6 % / CC1/2: 0.96 / Net I/σ(I): 14
Reflection shellResolution: 1.6→3.5 Å / Num. unique obs: 49269 / CC1/2: 0.94 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H30

6h30


Resolution: 1.6→38.66 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2 --
Rwork0.1 --
obs-49269 98.2 %
Displacement parametersBiso max: 112.37 Å2 / Biso mean: 27.05 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3444 0 76 261 3781

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