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- PDB-8b1d: DtpB-Nb132-APF -

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Basic information

Entry
Database: PDB / ID: 8b1d
TitleDtpB-Nb132-APF
Components
  • ALA-PRO-PHE
  • Dipeptide and tripeptide permease B
  • Nanobody 132
KeywordsMEMBRANE PROTEIN / MFS / Proton coupled Oligopeptide Transporter
Function / homology
Function and homology information


tripeptide transmembrane transport / dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / peptide transport / proton transmembrane transporter activity / proton transmembrane transport / protein transport / plasma membrane
Similarity search - Function
Amino acid/peptide transporter family, dipeptide/tripeptide permease B / : / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
DECANE / DODECANE / HEXANE / N-OCTANE / Dipeptide and tripeptide permease B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKiller, M. / Finocchio, G. / Lei, J. / Jungnickel, K. / Kotov, V. / Steinke, J. / Bartels, K. / Strauss, J. / Dupeux, F. / Humm, A.S. ...Killer, M. / Finocchio, G. / Lei, J. / Jungnickel, K. / Kotov, V. / Steinke, J. / Bartels, K. / Strauss, J. / Dupeux, F. / Humm, A.S. / Cornaciu, I. / Marquez, J. / Pardon, E. / Steyeart, J. / Loew, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2023
Title: Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition.
Authors: Kotov, V. / Killer, M. / Jungnickel, K.E.J. / Lei, J. / Finocchio, G. / Steinke, J. / Bartels, K. / Strauss, J. / Dupeux, F. / Humm, A.S. / Cornaciu, I. / Marquez, J.A. / Pardon, E. / Steyaert, J. / Low, C.
History
DepositionSep 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptide and tripeptide permease B
B: Nanobody 132
C: ALA-PRO-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,47118
Polymers67,7303
Non-polymers2,74215
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint9 kcal/mol
Surface area24060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.759, 125.156, 169.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein / Antibody / Protein/peptide / Sugars , 4 types, 4 molecules ABC

#1: Protein Dipeptide and tripeptide permease B


Mass: 53607.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dtpB, yhiP, b3496, JW3463 / Production host: Escherichia coli (E. coli) / References: UniProt: P36837
#2: Antibody Nanobody 132


Mass: 13788.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide ALA-PRO-PHE


Mass: 333.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 8 types, 140 molecules

#5: Chemical ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#8: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.3 Å3/Da / Density % sol: 71.38 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 100 mM HEPES pH 7.0, 30-40 % PEG 400 100-300 mM NaCl, 200 mM Li2SO4 and 25 mM APF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→62.58 Å / Num. obs: 100170 / % possible obs: 99.93 % / Redundancy: 2 % / Biso Wilson estimate: 57.56 Å2 / CC1/2: 1 / Net I/σ(I): 13.91
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 5217 / CC1/2: 0.609

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6gs4

6gs4


Resolution: 2.3→62.58 Å / SU ML: 0.3528 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2577 5006 5 %
Rwork0.2299 95164 -
obs0.2313 100170 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.08 Å2
Refinement stepCycle: LAST / Resolution: 2.3→62.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 186 126 4787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014772
X-RAY DIFFRACTIONf_angle_d1.31716425
X-RAY DIFFRACTIONf_chiral_restr0.0742730
X-RAY DIFFRACTIONf_plane_restr0.0098773
X-RAY DIFFRACTIONf_dihedral_angle_d17.32771678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.41671690.36363159X-RAY DIFFRACTION99.88
2.33-2.350.36171540.35363192X-RAY DIFFRACTION99.91
2.35-2.380.37841540.33633217X-RAY DIFFRACTION99.88
2.38-2.410.3151650.31463135X-RAY DIFFRACTION99.88
2.41-2.440.35161740.30033180X-RAY DIFFRACTION99.91
2.44-2.480.31091940.2933171X-RAY DIFFRACTION99.91
2.48-2.510.3181910.29133108X-RAY DIFFRACTION99.88
2.51-2.550.33541420.28363187X-RAY DIFFRACTION100
2.55-2.590.26861730.26673178X-RAY DIFFRACTION99.97
2.59-2.630.32451540.27713184X-RAY DIFFRACTION100
2.63-2.680.29551610.26443172X-RAY DIFFRACTION99.91
2.68-2.730.34561700.25633227X-RAY DIFFRACTION99.97
2.73-2.780.29641660.24723136X-RAY DIFFRACTION100
2.78-2.840.26441600.23443160X-RAY DIFFRACTION100
2.84-2.90.27961570.24013230X-RAY DIFFRACTION100
2.9-2.970.29391650.21483128X-RAY DIFFRACTION100
2.97-3.040.27831790.21463236X-RAY DIFFRACTION99.91
3.04-3.120.21921650.233089X-RAY DIFFRACTION100
3.12-3.210.27521730.2243216X-RAY DIFFRACTION99.97
3.21-3.320.29141640.23513139X-RAY DIFFRACTION100
3.32-3.440.26381870.24423183X-RAY DIFFRACTION100
3.44-3.570.28281910.23043136X-RAY DIFFRACTION100
3.57-3.740.22021250.21383193X-RAY DIFFRACTION100
3.74-3.930.27841750.20853184X-RAY DIFFRACTION100
3.93-4.180.23981700.21283175X-RAY DIFFRACTION99.94
4.18-4.50.23211470.21163193X-RAY DIFFRACTION99.94
4.5-4.950.2151450.18873203X-RAY DIFFRACTION100
4.95-5.670.21611700.21793153X-RAY DIFFRACTION99.91
5.67-7.140.24441880.23753153X-RAY DIFFRACTION99.97
7.14-62.580.24141780.23133147X-RAY DIFFRACTION99.31

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