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- PDB-8b5d: Exploring the ligand binding and conformational dynamics of recep... -

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Basic information

Entry
Database: PDB / ID: 8b5d
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
GLUTAMINE / DI(HYDROXYETHYL)ETHER / Glutamine transport system permease protein GlnP
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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)49,98814
Polymers49,0112
Non-polymers97712
Water3,873215
1
A: ABC transporter permease subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0007
Polymers24,5061
Non-polymers4946
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ABC transporter permease subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9887
Polymers24,5061
Non-polymers4826
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.610, 91.500, 57.910
Angle α, β, γ (deg.)90.000, 107.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 30 through 80 or resid 82 through 250 or resid 301 or resid 502))
21(chain B and (resid 30 through 80 or resid 82 through 301 or resid 404))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEU(chain A and (resid 30 through 80 or resid 82 through 250 or resid 301 or resid 502))AA30 - 804 - 54
12ASNASNTHRTHR(chain A and (resid 30 through 80 or resid 82 through 250 or resid 301 or resid 502))AA82 - 25056 - 224
13MPDMPDMPDMPD(chain A and (resid 30 through 80 or resid 82 through 250 or resid 301 or resid 502))AC401
14GOLGOLGOLGOL(chain A and (resid 30 through 80 or resid 82 through 250 or resid 301 or resid 502))AD402
21VALVALLEULEU(chain B and (resid 30 through 80 or resid 82 through 301 or resid 404))BB30 - 804 - 54
22ASNASNGOLGOL(chain B and (resid 30 through 80 or resid 82 through 301 or resid 404))BB - I82 - 40156
23GLNGLNGLNGLN(chain B and (resid 30 through 80 or resid 82 through 301 or resid 404))BL404

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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: 24505.615 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, 227 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM NaCl 50 mM TRIS 15 % MPD 20 % PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91587 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: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2→55.14 Å / Num. obs: 28607 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 36.05 Å2 / CC1/2: 0.95 / Net I/σ(I): 18
Reflection shellResolution: 2→4.5 Å / Num. unique obs: 27551 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H30

6h30


Resolution: 2→47.22 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 1376 5 %
Rwork0.1965 --
obs0.1998 27541 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.72 Å2 / Biso mean: 40.2771 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3411 0 83 215 3709
Biso mean--38.81 42.22 -
Num. residues----446
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1316X-RAY DIFFRACTION4.864TORSIONAL
12B1316X-RAY DIFFRACTION4.864TORSIONAL

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