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- PDB-8b1i: DtpB-Nb132-MS -

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Basic information

Entry
Database: PDB / ID: 8b1i
TitleDtpB-Nb132-MS
Components
  • Dipeptide and tripeptide permease B
  • MET-SER
  • 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: 2.55 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 13, 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: MET-SER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,37418
Polymers67,6323
Non-polymers2,74215
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint14 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.183, 124.675, 167.463
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 MET-SER


Mass: 236.289 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, 141 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.: 127 / 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: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 100 mM MES pH 6.0, 30-40 % PEG 400 100-300 mM NaCl, 200 mM BaCl2, and 20 mM MS

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Data collection

DiffractionMean temperature: 292 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 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.55→50.95 Å / Num. obs: 71403 / % possible obs: 99.92 % / Redundancy: 2 % / Biso Wilson estimate: 54.22 Å2 / CC1/2: 1 / Net I/σ(I): 9.44
Reflection shellResolution: 2.55→2.641 Å / Num. unique obs: 3707 / CC1/2: 0.545

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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: 2.55→50.95 Å / SU ML: 0.4004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1909
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2581 3458 4.84 %
Rwork0.2238 67945 -
obs0.2255 71403 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.75 Å2
Refinement stepCycle: LAST / Resolution: 2.55→50.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 186 127 4779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00964761
X-RAY DIFFRACTIONf_angle_d1.31416408
X-RAY DIFFRACTIONf_chiral_restr0.0768729
X-RAY DIFFRACTIONf_plane_restr0.0092770
X-RAY DIFFRACTIONf_dihedral_angle_d22.23411676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.580.37251570.34072702X-RAY DIFFRACTION99.58
2.58-2.620.38431490.33372683X-RAY DIFFRACTION99.96
2.62-2.660.34651340.31342754X-RAY DIFFRACTION100
2.66-2.70.34461460.3242752X-RAY DIFFRACTION99.97
2.7-2.750.37431290.32022644X-RAY DIFFRACTION99.96
2.75-2.790.38731360.2982738X-RAY DIFFRACTION100
2.79-2.850.30511560.29492759X-RAY DIFFRACTION100
2.85-2.90.3071410.28442662X-RAY DIFFRACTION100
2.9-2.960.29031260.2542696X-RAY DIFFRACTION99.89
2.96-3.020.29491500.24322764X-RAY DIFFRACTION100
3.02-3.090.35631180.24432699X-RAY DIFFRACTION100
3.09-3.170.29891170.23082796X-RAY DIFFRACTION99.93
3.17-3.260.24051320.23952680X-RAY DIFFRACTION100
3.26-3.350.30651340.24472723X-RAY DIFFRACTION100
3.35-3.460.26861260.20482734X-RAY DIFFRACTION100
3.46-3.580.21811540.18442720X-RAY DIFFRACTION99.97
3.58-3.730.22471210.18022723X-RAY DIFFRACTION100
3.73-3.90.22121350.18512746X-RAY DIFFRACTION99.97
3.9-4.10.21331340.18512699X-RAY DIFFRACTION100
4.1-4.360.21461430.18622716X-RAY DIFFRACTION100
4.36-4.70.22571110.17422747X-RAY DIFFRACTION100
4.7-5.170.19581280.18212720X-RAY DIFFRACTION100
5.17-5.910.22671720.22932697X-RAY DIFFRACTION100
5.92-7.450.28671620.23812704X-RAY DIFFRACTION100
7.46-50.950.2621470.24982687X-RAY DIFFRACTION99.23

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