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- PDB-4w6v: Crystal structure of a peptide transporter from Yersinia enteroco... -

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Basic information

Entry
Database: PDB / ID: 4w6v
TitleCrystal structure of a peptide transporter from Yersinia enterocolitica at 3 A resolution
ComponentsDi-/tripeptide transporter
KeywordsTRANSPORT PROTEIN / membrane protein / solute transporter / permease
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / protein transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; ...Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptide transporter YePEPT / Peptide transporter YePEPT
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. palearctica YE-P4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01819 Å
AuthorsJeckelmann, J.-M. / Boggavarapu, R. / Harder, D. / Ucurum, Z. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Bmc Biol. / Year: 2015
Title: Role of electrostatic interactions for ligand recognition and specificity of peptide transporters.
Authors: Boggavarapu, R. / Jeckelmann, J.M. / Harder, D. / Ucurum, Z. / Fotiadis, D.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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: Di-/tripeptide transporter


Theoretical massNumber of molelcules
Total (without water)56,5101
Polymers56,5101
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.656, 101.041, 104.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Di-/tripeptide transporter / Peptide Transporter


Mass: 56509.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Two missing loops
Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica YE-P4 (bacteria)
Gene: YEP4_02370 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R9G739, UniProt: A0A2R9TD79*PLUS

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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: 4.09 Å3/Da / Density % sol: 69.9 % / Description: orthorhombic
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4 / Details: PEG 300, NaCl, Li2SO4, LiH2PO4 / PH range: 4.0 - 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01819→46.2977 Å / Num. obs: 19398 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 104.04 Å2 / Net I/σ(I): 20
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.856.33.1550.22380437761.3523.1550.698
2.85-3.026.71.7980.42445536580.7491.7981.1100
3.02-3.236.90.9250.82379934480.3770.9252.2100
3.23-3.496.60.4181.82099332020.1760.4184.6100
3.49-3.826.70.1814.21967629510.0760.1819.9100
3.82-4.286.70.0829.21826727070.0340.08220100
4.28-4.946.40.04714.91536423920.020.04731.3100
4.94-6.056.60.04615.71349920490.0190.04631.899.9
6.05-8.556.20.02822.61000016170.0120.02843.499.7
8.55-46.2965.70.02214.153629380.0110.02267.499

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.73 Å46.3 Å
Translation7.73 Å46.3 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
XSCALEVERSION January 10, 2014data scaling
PHASER2.5.5phasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IKV

4ikv


Resolution: 3.01819→46.2977 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / Phase error: 33.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1833 5.07 %Random selection
Rwork0.2571 34355 --
obs0.259 19387 99.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 277.8 Å2 / Biso mean: 105.7227 Å2 / Biso min: 46.2 Å2
Refinement stepCycle: final / Resolution: 3.01819→46.2977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 0 0 3686
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053785
X-RAY DIFFRACTIONf_angle_d0.8895141
X-RAY DIFFRACTIONf_chiral_restr0.039593
X-RAY DIFFRACTIONf_plane_restr0.007626
X-RAY DIFFRACTIONf_dihedral_angle_d11.0551298
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0182-3.09980.39111350.36072564269997
3.0998-3.1910.35391380.331726382776100
3.191-3.29390.37781410.328826762817100
3.2939-3.41160.38121420.316326402782100
3.4116-3.54820.32881390.294626702809100
3.5482-3.70960.32611420.290126462788100
3.7096-3.90510.31681420.27726492791100
3.9051-4.14960.28131440.271926592803100
4.1496-4.46980.27741440.237526282772100
4.4698-4.91910.23951400.213526432783100
4.9191-5.62990.34581440.252326572801100
5.6299-7.08890.30931410.272826572798100
7.0889-46.30320.24841410.22712628276999

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