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- PDB-6hzp: Crystal structure of a POT family transporter in complex with 5-a... -

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Basic information

Entry
Database: PDB / ID: 6hzp
TitleCrystal structure of a POT family transporter in complex with 5-aminolevulinic acid
ComponentsPeptide ABC transporter permease
KeywordsMEMBRANE PROTEIN / POT / SLC15 / Proton coupled transport / prodrug
Function / homology
Function and homology information


peptide transmembrane transporter activity / peptide transport / 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
5-azanyl-4-oxidanylidene-pentanoic acid / 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: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural basis for prodrug recognition by the SLC15 family of proton-coupled peptide transporters.
Authors: Minhas, G.S. / Newstead, S.
History
DepositionOct 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 23, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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

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Assembly

Deposited unit
A: Peptide ABC transporter permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0112
Polymers53,8801
Non-polymers1311
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 57.060, 99.500
Angle α, β, γ (deg.)90.000, 104.980, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Peptide ABC transporter permease / POT family transporter / PepTSh


Mass: 53879.969 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-FVT / 5-azanyl-4-oxidanylidene-pentanoic acid


Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 3.06 Å3/Da / Density % sol: 59.74 %
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: 40mM 5-aminolevulinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872899 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872899 Å / Relative weight: 1
ReflectionResolution: 2.5→49.06 Å / Num. obs: 22767 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 56.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.062 / Rrim(I) all: 0.159 / Net I/σ(I): 8.9 / Num. measured all: 150287
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.66.61.3761702125630.6350.5731.4931.3100
9.01-49.066.10.0432175250.9990.0170.0443199.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.27data scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EXS

6exs


Resolution: 2.5→36.76 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.894 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.368 / SU Rfree Blow DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1140 5.02 %RANDOM
Rwork0.22 ---
obs0.221 22724 99.8 %-
Displacement parametersBiso max: 163.99 Å2 / Biso mean: 65.91 Å2 / Biso min: 33.46 Å2
Baniso -1Baniso -2Baniso -3
1-8.4219 Å20 Å27.5471 Å2
2---10.5036 Å20 Å2
3---2.0817 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.5→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3790 0 9 31 3830
Biso mean--93.3 53.03 -
Num. residues----487
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1705SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1157HARMONIC5
X-RAY DIFFRACTIONt_it7852HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion525SEMIHARMONIC5
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_contact7989SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7852HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg14236HARMONIC20.85
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion15.84
LS refinement shellResolution: 2.5→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2312 21 4.62 %
Rwork0.2078 434 -
all0.209 455 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 20.141 Å / Origin y: 0.998 Å / Origin z: 25.8664 Å
111213212223313233
T-0.3294 Å2-0.0031 Å2-0.0557 Å2--0.0972 Å20.0021 Å2---0.2586 Å2
L1.8887 °20.0574 °20.3449 °2-0.7816 °20.3173 °2--1.5393 °2
S-0.103 Å °0.1556 Å °0.0026 Å °-0.1559 Å °0.0408 Å °0.0612 Å °-0.1637 Å °0.023 Å °0.0622 Å °
Refinement TLS groupSelection details: { A|* }

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