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- PDB-8b1g: DtpB-Nb132-AW -

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Basic information

Entry
Database: PDB / ID: 8b1g
TitleDtpB-Nb132-AW
Components
  • ALA-TRP
  • 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 / proton transmembrane transporter activity / proton transmembrane transport / protein transport / membrane / 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: 2.5 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

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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-TRP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,41318
Polymers67,6713
Non-polymers2,74215
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint12 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.614, 126.408, 168.039
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-TRP


Mass: 275.303 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, 138 molecules

#5: Chemical ChemComp-OCT / N-OCTANE / 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 / Polyethylene 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 / Polyethylene glycol


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 / 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.29 Å3/Da / Density % sol: 71.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 100 mM HEPES pH 7.0, 30-40 % PEG 400 100-300 mM NaCl, 200 mM Li2SO4 and 10 mM AW

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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: May 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→69.97 Å / Num. obs: 77038 / % possible obs: 99.15 % / Redundancy: 2 % / Biso Wilson estimate: 69.68 Å2 / CC1/2: 1 / Net I/σ(I): 12.36
Reflection shellResolution: 2.5→2.589 Å / Num. unique obs: 4000 / CC1/2: 0.432

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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: 2.5→69.97 Å / SU ML: 0.3661 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.1074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 3805 4.94 %
Rwork0.2251 73233 -
obs0.2263 77038 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→69.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4471 0 186 124 4781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044768
X-RAY DIFFRACTIONf_angle_d1.33846420
X-RAY DIFFRACTIONf_chiral_restr0.0758729
X-RAY DIFFRACTIONf_plane_restr0.0092771
X-RAY DIFFRACTIONf_dihedral_angle_d17.44651674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.530.38391510.35762598X-RAY DIFFRACTION95.85
2.53-2.560.32081270.33932722X-RAY DIFFRACTION99.37
2.56-2.60.34671300.33732808X-RAY DIFFRACTION99.76
2.6-2.640.30841150.3212722X-RAY DIFFRACTION99.89
2.64-2.680.32051510.31052681X-RAY DIFFRACTION99.93
2.68-2.720.3081460.29092787X-RAY DIFFRACTION100
2.72-2.760.31021550.27382701X-RAY DIFFRACTION100
2.76-2.810.3191500.26222741X-RAY DIFFRACTION99.97
2.81-2.860.26361690.24982747X-RAY DIFFRACTION99.93
2.86-2.920.25541680.2352655X-RAY DIFFRACTION100
2.92-2.980.26011350.22872735X-RAY DIFFRACTION99.97
2.98-3.040.28071360.22432806X-RAY DIFFRACTION99.97
3.04-3.110.23851340.21992691X-RAY DIFFRACTION100
3.11-3.190.27171060.21342809X-RAY DIFFRACTION100
3.19-3.280.2521430.21462718X-RAY DIFFRACTION99.97
3.28-3.370.28481370.22312737X-RAY DIFFRACTION100
3.37-3.480.22591470.21682731X-RAY DIFFRACTION99.97
3.48-3.610.21991250.20072779X-RAY DIFFRACTION99.97
3.61-3.750.2681290.21042196X-RAY DIFFRACTION81.38
3.75-3.920.23291310.20672763X-RAY DIFFRACTION99.97
3.92-4.130.21611310.20072734X-RAY DIFFRACTION100
4.13-4.390.23251670.20462711X-RAY DIFFRACTION100
4.39-4.720.21671480.18822724X-RAY DIFFRACTION99.97
4.72-5.20.19441280.19982756X-RAY DIFFRACTION100
5.2-5.950.26751640.23452729X-RAY DIFFRACTION100
5.95-7.490.2661430.23842727X-RAY DIFFRACTION100
7.5-69.970.25021390.23722725X-RAY DIFFRACTION99.03

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