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- PDB-5oqt: Crystal structure of a bacterial cationic amino acid transporter ... -

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Basic information

Entry
Database: PDB / ID: 5oqt
TitleCrystal structure of a bacterial cationic amino acid transporter (CAT) homologue
Components
  • Amino acid transporter
  • Uncharacterized protein YneM
KeywordsTRANSPORT PROTEIN / SLC7 / APC / LeuT fold
Function / homology
Function and homology information


cellular response to magnesium starvation / magnesium ion homeostasis / amino acid transmembrane transporter activity / membrane / plasma membrane
Similarity search - Function
: / Small protein MgtS-like / Amino acid/polyamine transporter I / Amino acid permease
Similarity search - Domain/homology
ACETATE ION / ALANINE / CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Small protein MgtS / Amino acid transporter
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsJungnickel, K.E.J. / Newstead, S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
European CommissionNanoMem United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for amino acid transport by the CAT family of SLC7 transporters.
Authors: Jungnickel, K.E.J. / Parker, J.L. / Newstead, S.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Feb 28, 2018Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Apr 25, 2018Group: Data collection / Category: reflns_shell
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rpim_I_all
Revision 1.4Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Amino acid transporter
C: Uncharacterized protein YneM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,52419
Polymers54,3192
Non-polymers5,20517
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-30 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.923, 83.148, 119.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein Amino acid transporter


Mass: 50807.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Gene: GK0930 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q5L1G5
#2: Protein/peptide Uncharacterized protein YneM


Mass: 3511.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: yneM, b4599, JW1527.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A5A616

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Non-polymers , 6 types, 125 molecules

#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H7NO2 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
#7: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.51 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / pH: 4
Details: 28-34 % PEG 400, 0.1 M sodium acetate pH 4.0, 0.1 M potassium fluoride, containing 10 mM of the amino acid ligand.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.86→64.72 Å / Num. obs: 18307 / % possible obs: 99 % / Redundancy: 5.2 % / Biso Wilson estimate: 68 Å2 / CC1/2: 0.86 / Rmerge(I) obs: 0.1523 / Rpim(I) all: 0.077 / Net I/σ(I): 6.3
Reflection shellResolution: 2.86→2.96 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.789 / Num. unique obs: 1770 / CC1/2: 0.51 / Rpim(I) all: 0.842 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GIA

3gia


Resolution: 2.86→64.72 Å / Cor.coef. Fo:Fc: 0.9054 / Cor.coef. Fo:Fc free: 0.9229 / SU R Cruickshank DPI: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.044 / SU Rfree Blow DPI: 0.366 / SU Rfree Cruickshank DPI: 0.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 901 4.95 %RANDOM
Rwork0.215 ---
obs0.2178 18190 99.18 %-
Displacement parametersBiso mean: 79.97 Å2
Baniso -1Baniso -2Baniso -3
1--17.1267 Å20 Å20 Å2
2--7.5751 Å20 Å2
3---9.5516 Å2
Refine analyzeLuzzati coordinate error obs: 0.456 Å
Refinement stepCycle: 1 / Resolution: 2.86→64.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 329 108 4128
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014102HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15508HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1461SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes45HARMONIC2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it4102HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.38
X-RAY DIFFRACTIONt_other_torsion20.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion526SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4965SEMIHARMONIC4
LS refinement shellResolution: 2.86→3.03 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3163 138 4.83 %
Rwork0.2641 2717 -
all0.2667 2855 -
obs--99.18 %
Refinement TLS params.Method: refined / Origin x: -12.4873 Å / Origin y: -3.6368 Å / Origin z: 25.1452 Å
111213212223313233
T0.2198 Å2-0.0733 Å2-0.0194 Å2--0.0852 Å20.0711 Å2---0.3603 Å2
L1.2666 °20.0471 °20.26 °2-2.0839 °20.4373 °2--2.3701 °2
S0.1187 Å °0.0227 Å °-0.04 Å °-0.239 Å °-0.0139 Å °0.1435 Å °0.1775 Å °-0.3613 Å °-0.1048 Å °
Refinement TLS groupSelection details: { A|* }

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