[English] 日本語
Yorodumi
- PDB-5mmt: Inward open PepTSt from Streptococcus thermophilus crystallized i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mmt
TitleInward open PepTSt from Streptococcus thermophilus crystallized in space group P3121
ComponentsDi-or tripeptide:H+ symporter
KeywordsTRANSPORT PROTEIN / Integral membrane protein / Major facilitator superfamily transporter (MFS transporter) / POT PTR or PepT family / proton-coupled peptide transporter
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / peptide transport / 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
Di-or tripeptide:H+ symporter
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.4 Å
AuthorsQuistgaard, E.M. / Molledo, M.M. / Nordlund, P. / Loew, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2013-5905 Sweden
European Communitys Seventh Framework Programme (FP7/2007-2013) under BioStruct-X
CitationJournal: PLoS ONE / Year: 2017
Title: Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121.
Authors: Quistgaard, E.M. / Martinez Molledo, M. / Low, C.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)53,6481
Polymers53,6481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.190, 80.190, 293.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#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)
Gene: dtpT, stu0970 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5M4H8

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.08 Å3/Da / Density % sol: 75.79 % / Description: Rod-shaped crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.05 M HEPES pH 8.0, 30% PEG550 MME, 1.2% Fos-Choline 10

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.4→44.85 Å / Num. obs: 11881 / % possible obs: 74.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 96.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rsym value: 0.08 / Net I/σ(I): 13.67
Reflection shellResolution: 3.4→3.49 Å / Redundancy: 0.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.13 / CC1/2: 0.834 / % possible all: 5.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.4→44.85 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / Phase error: 36.6
Details: The data set used for refinement was truncated and anisotropically scaled using the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/). Cut-off values for truncation: ...Details: The data set used for refinement was truncated and anisotropically scaled using the Diffraction Anisotropy Server (https://services.mbi.ucla.edu/anisoscale/). Cut-off values for truncation: 3.9 A in the a-direction, 3.7 A in the b-direction and 3.4 A in the best diffracting c-direction of the crystal.
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 589 4.96 %Random
Rwork0.2652 ---
obs0.2662 11292 74.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 127.1 Å2
Refinement stepCycle: LAST / Resolution: 3.4→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 0 3283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053377
X-RAY DIFFRACTIONf_angle_d1.1884604
X-RAY DIFFRACTIONf_dihedral_angle_d11.4821132
X-RAY DIFFRACTIONf_chiral_restr0.045538
X-RAY DIFFRACTIONf_plane_restr0.006552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.74050.3994340.3201641X-RAY DIFFRACTION17.4
3.7405-4.28130.32161540.27242964X-RAY DIFFRACTION80
4.2813-5.39260.25791950.23343768X-RAY DIFFRACTION99.9
5.3926-44.850.28542060.28023916X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 85.5225 Å / Origin y: -29.2027 Å / Origin z: 25.7457 Å
111213212223313233
T1.3796 Å2-0.6503 Å2-0.3807 Å2-0.5457 Å20.0886 Å2--0.5299 Å2
L5.4879 °21.1137 °21.3581 °2-3.2331 °21.4566 °2--5.2727 °2
S-0.3592 Å °0.6528 Å °-0.0744 Å °-1.3202 Å °0.5745 Å °0.0902 Å °-0.1144 Å °0.0518 Å °-0.0971 Å °
Refinement TLS groupSelection details: chain 'A'

+
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