[English] 日本語
Yorodumi
- PDB-6e9o: E. coli D-galactonate:proton symporter mutant E133Q in the outwar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6e9o
TitleE. coli D-galactonate:proton symporter mutant E133Q in the outward substrate-bound form
ComponentsD-galactonate transport
KeywordsMEMBRANE PROTEIN / MFS Transporter / SLC17 / organic anion transporter
Function / homologyMajor facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / transmembrane transporter activity / plasma membrane / D-galactonic acid / D-galactonate transport
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.501 Å
AuthorsLeano, J.B. / Edwards, R.H. / Stroud, R.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH50712 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM24485 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS089713 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM024485-37S1 United States
CitationJournal: Plos Biol. / Year: 2019
Title: Structures suggest a mechanism for energy coupling by a family of organic anion transporters.
Authors: Leano, J.B. / Batarni, S. / Eriksen, J. / Juge, N. / Pak, J.E. / Kimura-Someya, T. / Robles-Colmenares, Y. / Moriyama, Y. / Stroud, R.M. / Edwards, R.H.
History
DepositionAug 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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
B: D-galactonate transport
A: D-galactonate transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3974
Polymers101,0052
Non-polymers3922
Water362
1
B: D-galactonate transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6992
Polymers50,5021
Non-polymers1961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: D-galactonate transport
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6992
Polymers50,5021
Non-polymers1961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)217.070, 70.710, 107.160
Angle α, β, γ (deg.)90.00, 101.81, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein D-galactonate transport / D-galactonate transporter


Mass: 50502.375 Da / Num. of mol.: 2 / Mutation: E133Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dgoT, BN17_36391, HMPREF3040_00185 / Production host: Escherichia coli (E. coli) / References: UniProt: J7QAK3
#2: Chemical ChemComp-J0M / D-galactonic acid / D-galactonate


Mass: 196.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.12 Å3/Da / Density % sol: 70.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 100mM glycine pH 9, 32% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 3.5→106.23 Å / Num. obs: 20394 / % possible obs: 99.8 % / Redundancy: 3.5 % / CC1/2: 1 / Rrim(I) all: 0.08 / Net I/σ(I): 10.7
Reflection shellResolution: 3.5→3.77 Å / Num. unique obs: 4030 / CC1/2: 0.159 / Rrim(I) all: 5.15

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E9N

6e9n


Resolution: 3.501→14.984 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3 1843 10 %
Rwork0.2846 --
obs0.2862 18431 91.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.501→14.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6138 0 26 2 6166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036342
X-RAY DIFFRACTIONf_angle_d0.618639
X-RAY DIFFRACTIONf_dihedral_angle_d11.3212119
X-RAY DIFFRACTIONf_chiral_restr0.037993
X-RAY DIFFRACTIONf_plane_restr0.0041043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.501-3.59440.4802230.4352236X-RAY DIFFRACTION17
3.5944-3.69860.38671290.42391145X-RAY DIFFRACTION82
3.6986-3.81610.42171460.41341298X-RAY DIFFRACTION96
3.8161-3.95010.38211520.3681364X-RAY DIFFRACTION99
3.9501-4.10510.37581550.34461393X-RAY DIFFRACTION100
4.1051-4.28780.35891520.31431371X-RAY DIFFRACTION100
4.2878-4.5080.3431540.29691388X-RAY DIFFRACTION99
4.508-4.78180.31321520.26621377X-RAY DIFFRACTION100
4.7818-5.13720.35991540.27311383X-RAY DIFFRACTION100
5.1372-5.62910.32471550.29711397X-RAY DIFFRACTION100
5.6291-6.38770.31361580.30541420X-RAY DIFFRACTION100
6.3877-7.85040.2791550.27991391X-RAY DIFFRACTION100
7.8504-14.98440.24461580.25141425X-RAY DIFFRACTION99

+
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