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- PDB-6exs: Crystal structure of a POT family transporter in complex with thi... -

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Basic information

Entry
Database: PDB / ID: 6exs
TitleCrystal structure of a POT family transporter in complex with thioalcohol conjugated peptide.
ComponentsPeptide ABC transporter permease
KeywordsMEMBRANE PROTEIN / Major Facilitator Superfamily / POT transporter / conjugated peptide ligand
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Dipeptide/tripeptide permease / MFS general substrate transporter like domains / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-C3H / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Peptide ABC transporter permease / Peptide ABC transporter permease
Similarity search - Component
Biological speciesStaphylococcus hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMinhas, G.S. / Newstead, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust102890/Z/13/Z United Kingdom
CitationJournal: Elife / Year: 2018
Title: Structural basis of malodour precursor transport in the human axilla.
Authors: Minhas, G.S. / Bawdon, D. / Herman, R. / Rudden, M. / Stone, A.P. / James, A.G. / Thomas, G.H. / Newstead, S.
History
DepositionNov 9, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jan 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: Peptide ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,74915
Polymers53,8221
Non-polymers4,92714
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.040, 55.576, 100.866
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide ABC transporter permease


Mass: 53821.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus hominis (bacteria) / Gene: BL313_09825 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: A0A1L8Y4Q3, UniProt: A0A657M1C3*PLUS
#2: 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
#3: Chemical ChemComp-C3H / 2-[[(2~{R})-2-azanyl-3-[(3~{S})-3-methyl-1-oxidanyl-hexan-3-yl]sulfanyl-propanoyl]amino]ethanoic acid


Mass: 292.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5
Details: 26-27% (v/v) PEG 200, 220 mM (NH4)2HPO4, and 110 mM sodium citrate (pH 5.0). Ligand: 5mM CG-3M3SH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872899 Å / Relative weight: 1
ReflectionResolution: 2.4→48.29 Å / Num. obs: 25401 / % possible obs: 99.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 54.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.194 / Rpim(I) all: 0.08 / Rrim(I) all: 0.211 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.6 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.4-2.492.05826230.4120.8512.2399.8
8.98-48.290.0385220.9990.0160.04199.5

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2B

4d2b


Resolution: 2.5→48.29 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.903 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.435 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.411 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.251
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1137 5.07 %RANDOM
Rwork0.211 ---
obs0.212 22408 99.5 %-
Displacement parametersBiso mean: 57.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.5837 Å20 Å2-0.0973 Å2
2--1.257 Å20 Å2
3----3.8407 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.5→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 227 76 4093
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014104HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045513HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1473SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes590HARMONIC5
X-RAY DIFFRACTIONt_it4104HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion17.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion541SEMIHARMONIC5
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_contact5015SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.62 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.246 151 5.12 %
Rwork0.21 2799 -
all0.212 2950 -
obs--99.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3461-0.16970.23410.9490.25081.2932-0.04570.09710.039-0.18850.08160.0363-0.14740.0351-0.0359-0.2562-0.0304-0.00550.04010.0101-0.155519.80382.869626.6288
20.75930.48820.58860.1788-0.2630.5571-0.0082-0.00370.0001-0.02980.0190.0073-0.0107-0.012-0.01080.0057-0.03590.0495-0.0198-0.0535-0.101123.69480.045631.7668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ A|501-513}

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