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- PDB-4q65: Structure of the E. coli Peptide Transporter YbgH -

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Basic information

Entry
Database: PDB / ID: 4q65
TitleStructure of the E. coli Peptide Transporter YbgH
ComponentsDipeptide permease D
KeywordsTRANSPORT PROTEIN / MFS fold motif A / peptide transporter
Function / homology
Function and homology information


oligopeptide transmembrane transporter activity / dipeptide transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / peptide transmembrane transporter activity / plasma membrane => GO:0005886 / protein transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Amino acid/peptide transporter family, dipeptide permease D / 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. ...Amino acid/peptide transporter family, dipeptide permease D / 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
Dipeptide permease D
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsZhang, C. / Zhao, Y. / Mao, G. / Liu, M. / Wang, X.
CitationJournal: Structure / Year: 2014
Title: Crystal structure of the E. coli peptide transporter YbgH.
Authors: Zhao, Y. / Mao, G. / Liu, M. / Zhang, L. / Wang, X. / Zhang, X.C.
History
DepositionApr 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptide permease D


Theoretical massNumber of molelcules
Total (without water)54,1841
Polymers54,1841
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.035, 109.448, 76.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Dipeptide permease D


Mass: 54183.594 Da / Num. of mol.: 1 / Mutation: L472V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dtpD, ybgH, b0709, JW0699 / Production host: Escherichia coli (E. coli) / References: UniProt: P75742

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.21 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50mM NaAc (pH 5.0), 25%(v/v) PEG400, 50mM Mg(Ac)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-17A10.9788
SYNCHROTRONSSRF BL17U21
SYNCHROTRONSPring-8 BL41XU31.006
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 12, 2012
2
3
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2x-ray1
3x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
211
31.0061
ReflectionResolution: 3.4→50 Å / Num. obs: 9105 / % possible obs: 72 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
3.4-3.7145.3
3.7-4.2155.6
4.2-4.9178.4
4.9-7.1197.8
7.1-50188.4

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Processing

Software
NameVersionClassification
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.4→44.54 Å / SU ML: 0.56 / σ(F): 1.33 / Phase error: 39.36 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.3157 753 4.82 %
Rwork0.2576 --
obs0.2603 9105 74.21 %
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 0 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073447
X-RAY DIFFRACTIONf_angle_d1.2734687
X-RAY DIFFRACTIONf_dihedral_angle_d16.9671158
X-RAY DIFFRACTIONf_chiral_restr0.097550
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.66250.39711230.33552023X-RAY DIFFRACTION51
3.6625-4.03090.35981200.30462422X-RAY DIFFRACTION61
4.0309-4.61360.30991450.2432983X-RAY DIFFRACTION75
4.6136-5.81060.31011930.26323778X-RAY DIFFRACTION94
5.8106-44.54350.3011720.24253648X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 190.9846 Å / Origin y: 27.9697 Å / Origin z: 99.3857 Å
111213212223313233
T0.4793 Å2-0.0109 Å2-0.0468 Å2-0.5605 Å2-0.0885 Å2--0.5548 Å2
L2.7207 °20.5721 °20.4732 °2-5.3523 °2-0.1811 °2--2.923 °2
S-0.184 Å °0.6597 Å °-0.0367 Å °-0.0923 Å °0.0201 Å °-0.2001 Å °0.0874 Å °0.3984 Å °0.1438 Å °
Refinement TLS groupSelection details: chain A

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