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- PDB-8b1c: DtpB-Nb132-ALA -

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Basic information

Entry
Database: PDB / ID: 8b1c
TitleDtpB-Nb132-ALA
Components
  • ALA-LEU-ALA
  • 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: 2.56 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 20, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,41118
Polymers67,6703
Non-polymers2,74215
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint13 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.396, 123.541, 169.331
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-LEU-ALA


Mass: 273.329 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, 134 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.: 120 / 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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion
Details: 100 mM Hepes pH 6.7, 30-40 % PEG 400 100-300 mM NaCl, 100-300 mM MgCl2, 10 mM ALA

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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: Apr 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.56→51.79 Å / Num. obs: 70999 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 66.52 Å2 / CC1/2: 0.999 / Net I/σ(I): 16.74
Reflection shellResolution: 2.56→2.651 Å / Num. unique obs: 3699 / CC1/2: 0.694

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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: 2.56→51.79 Å / SU ML: 0.316 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.6967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.241 3561 5.02 %
Rwork0.2149 67438 -
obs0.2163 70999 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.22 Å2
Refinement stepCycle: LAST / Resolution: 2.56→51.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 186 120 4776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01064765
X-RAY DIFFRACTIONf_angle_d1.39676415
X-RAY DIFFRACTIONf_chiral_restr0.0819731
X-RAY DIFFRACTIONf_plane_restr0.01771
X-RAY DIFFRACTIONf_dihedral_angle_d20.59081675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.60.31021400.30212728X-RAY DIFFRACTION99.79
2.6-2.630.32941480.29752639X-RAY DIFFRACTION99.82
2.63-2.670.31961380.27832699X-RAY DIFFRACTION100
2.67-2.710.33391560.27862717X-RAY DIFFRACTION100
2.71-2.760.28171590.26652635X-RAY DIFFRACTION99.96
2.76-2.810.30881090.25792751X-RAY DIFFRACTION99.9
2.81-2.860.25481550.25672725X-RAY DIFFRACTION100
2.86-2.910.29591580.24532655X-RAY DIFFRACTION99.96
2.91-2.970.23131080.23172724X-RAY DIFFRACTION100
2.97-3.040.24831570.21742718X-RAY DIFFRACTION100
3.04-3.110.25021270.2212669X-RAY DIFFRACTION100
3.11-3.180.2811370.21442769X-RAY DIFFRACTION100
3.18-3.270.24031110.21372667X-RAY DIFFRACTION100
3.27-3.370.22821480.2062756X-RAY DIFFRACTION100
3.37-3.470.27831410.22032661X-RAY DIFFRACTION100
3.47-3.60.24291500.2152722X-RAY DIFFRACTION100
3.6-3.740.24881450.21452680X-RAY DIFFRACTION100
3.74-3.910.24011490.19952697X-RAY DIFFRACTION100
3.91-4.120.21951690.19982662X-RAY DIFFRACTION99.72
4.12-4.380.2461470.19012674X-RAY DIFFRACTION100
4.38-4.710.2081370.1882716X-RAY DIFFRACTION100
4.71-5.190.18511260.18682692X-RAY DIFFRACTION99.86
5.19-5.930.26651550.22672703X-RAY DIFFRACTION100
5.94-7.480.21421330.22932711X-RAY DIFFRACTION99.93
7.48-51.790.23561580.21492668X-RAY DIFFRACTION99.3

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