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- PDB-8b1k: DtpB-Nb132-NV -

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Basic information

Entry
Database: PDB / ID: 8b1k
TitleDtpB-Nb132-NV
Components
  • ASN-VAL
  • 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 / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
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: 2.8 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

Downloads & links

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Assembly

Deposited unit
A: Dipeptide and tripeptide permease B
B: Nanobody 132
C: ASN-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,36918
Polymers67,6273
Non-polymers2,74215
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint15 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.138, 124.925, 165.773
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 ASN-VAL


Mass: 231.249 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, 145 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.: 131 / 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: 4.14 Å3/Da / Density % sol: 70.32 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 100 mM HEPES pH 6.7, 30-40 % PEG 400 100-300 mM NaCl, 100-300 mM MgCl2, and 10 mM of NV

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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: Feb 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→54.14 Å / Num. obs: 53377 / % possible obs: 99.77 % / Redundancy: 2 % / Biso Wilson estimate: 77.16 Å2 / CC1/2: 1 / Net I/σ(I): 12.01
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 2811 / CC1/2: 0.367

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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: 2.8→54.14 Å / SU ML: 0.4593 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.177
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2504 2600 4.87 %
Rwork0.226 50777 -
obs0.2272 53377 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→54.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4467 0 186 131 4784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01194762
X-RAY DIFFRACTIONf_angle_d1.51826411
X-RAY DIFFRACTIONf_chiral_restr0.0882730
X-RAY DIFFRACTIONf_plane_restr0.0107771
X-RAY DIFFRACTIONf_dihedral_angle_d15.8611675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.850.42831370.39122688X-RAY DIFFRACTION99.23
2.85-2.910.38941220.37742658X-RAY DIFFRACTION99.29
2.91-2.970.33211570.33012688X-RAY DIFFRACTION99.93
2.97-3.030.32661080.32352677X-RAY DIFFRACTION99.32
3.03-3.10.33641470.32012629X-RAY DIFFRACTION99.93
3.1-3.180.35351510.28632679X-RAY DIFFRACTION99.75
3.18-3.260.28581420.2842612X-RAY DIFFRACTION99.71
3.26-3.360.29931370.27832737X-RAY DIFFRACTION99.86
3.36-3.470.31591250.25242673X-RAY DIFFRACTION100
3.47-3.590.27021470.2272676X-RAY DIFFRACTION99.93
3.59-3.740.23821430.21042625X-RAY DIFFRACTION99.96
3.74-3.910.29221360.19022719X-RAY DIFFRACTION100
3.91-4.110.22251180.18362711X-RAY DIFFRACTION100
4.11-4.370.21221520.18962636X-RAY DIFFRACTION99.89
4.37-4.710.2281570.16412657X-RAY DIFFRACTION99.89
4.71-5.180.22951130.18362693X-RAY DIFFRACTION100
5.18-5.930.22281190.22282712X-RAY DIFFRACTION100
5.93-7.460.22531480.22662655X-RAY DIFFRACTION100
7.47-54.140.21271410.22652652X-RAY DIFFRACTION98.87

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