[English] 日本語
Yorodumi
- PDB-8b1c: DtpB-Nb132-ALA -

+
Open data


ID or keywords:

Loading...

-
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 / 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: 2.56 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more