[English] 日本語
Yorodumi
- PDB-5oxm: PepTSt in complex with dipeptide Asp-Glu -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5oxm
TitlePepTSt in complex with dipeptide Asp-Glu
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Alpha-helical protein / membrane protein / MFS fold / peptide transporter
Function / homology
Function and homology information


tripeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / identical protein binding / plasma membrane
Similarity search - Function
: / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / Major facilitator superfamily domain ...: / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / ASPARTIC ACID / GLUTAMIC ACID / PHOSPHATE ION / Di-/tripeptide transporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsMartinez Molledo, M. / Quistgaard, E.M. / Loew, C.
CitationJournal: Structure / Year: 2018
Title: Multispecific Substrate Recognition in a Proton-Dependent Oligopeptide Transporter.
Authors: Martinez Molledo, M. / Quistgaard, E.M. / Flayhan, A. / Pieprzyk, J. / Low, C.
History
DepositionSep 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_PDB_atom_name / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Di-or tripeptide:H+ symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,34023
Polymers53,6481
Non-polymers5,69122
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: micro scale thermophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-26 kcal/mol
Surface area20570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.600, 109.000, 107.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-628-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Di-or tripeptide:H+ symporter


Mass: 53648.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (bacteria)
Strain: ATCC BAA-250 / LMG 18311 / Gene: dtpT, stu0970 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q5M4H8

-
Non-polymers , 6 types, 51 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C18H34O4
#4: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O4
#5: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#6: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 292.15 K / Method: lipidic cubic phase
Details: 0.1 M HEPES pH 7.0, 0.25 M ammonium phosphate monobasic, 21% PEG 400, 10 mM Asp-Glu

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.0396 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0396 Å / Relative weight: 1
ReflectionResolution: 2.295→48.57 Å / Num. obs: 26529 / % possible obs: 98.99 % / Redundancy: 6.5 % / Biso Wilson estimate: 53.66 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1073 / Net I/σ(I): 10.33
Reflection shellResolution: 2.295→2.377 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.03 / Num. unique obs: 2526 / CC1/2: 0.509 / % possible all: 95.06

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D2B

4d2b


Resolution: 2.295→48.563 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.16
RfactorNum. reflection% reflection
Rfree0.2353 1321 5 %
Rwork0.2146 --
obs0.2157 26403 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→48.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 372 29 3813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053866
X-RAY DIFFRACTIONf_angle_d0.9165170
X-RAY DIFFRACTIONf_dihedral_angle_d16.8831386
X-RAY DIFFRACTIONf_chiral_restr0.032571
X-RAY DIFFRACTIONf_plane_restr0.004610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.295-2.38690.38871410.32482667X-RAY DIFFRACTION96
2.3869-2.49550.28771430.28432751X-RAY DIFFRACTION99
2.4955-2.62710.34091460.2682763X-RAY DIFFRACTION99
2.6271-2.79170.28621480.2492775X-RAY DIFFRACTION100
2.7917-3.00720.25741450.23022782X-RAY DIFFRACTION100
3.0072-3.30970.2351460.21332784X-RAY DIFFRACTION100
3.3097-3.78850.23041480.19392798X-RAY DIFFRACTION99
3.7885-4.77250.21871500.19062845X-RAY DIFFRACTION100
4.7725-48.57420.19851540.21042917X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.60340.026-1.32652.4673-1.3151.9938-0.08750.0644-0.0238-0.28070.14140.40710.2553-0.0954-0.02430.3466-0.0105-0.020.34170.00820.43835.027616.1302-5.5245
24.4872-0.6762-0.87341.94720.77083.8048-0.00550.73790.7215-0.48990.26050.185-0.4589-0.2042-0.16120.4408-0.0005-0.00130.4260.04840.447323.747830.04260.1871
35.39660.994-2.07163.4388-1.19841.6537-0.16231.16110.0369-0.59480.27890.17430.0285-0.7391-0.04830.39670.0104-0.00530.6557-0.01450.358113.391822.38062.1555
40.0940.1013-0.08620.1043-0.10370.12450.0044-0.00190.0179-0.0763-0.0801-0.0638-0.0094-0.0451-00.9246-0.14-0.26661.35450.03910.972723.268817.0282-3.1613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 241 )
2X-RAY DIFFRACTION2chain 'A' and (resid 242 through 320 )
3X-RAY DIFFRACTION3chain 'A' and (resid 321 through 472 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 2 )

+
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