[English] 日本語
Yorodumi
- PDB-7e9y: Crystal structure of eLACCO1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7e9y
TitleCrystal structure of eLACCO1
ComponentsLactate-binding periplasmic protein TTHA0766,Lactate-binding periplasmic protein TTHA0766
KeywordsFLUORESCENT PROTEIN / Biosensor / genetically encoded fluorescent biosensor / extracellular / L-lactate
Function / homology
Function and homology information


lactate transport / tripartite ATP-independent periplasmic transporter complex / transmembrane transport / periplasmic space / calcium ion binding / protein homodimerization activity / zinc ion binding
Similarity search - Function
Lactate-binding periplasmic protein TTHA0766 / Solute binding protein, TakP-like / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / Lactate-binding periplasmic protein TTHA0766
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Thermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWen, Y. / Campbell, R.E. / Lemieux, M.J. / Nasu, Y.
CitationJournal: Nat Commun / Year: 2021
Title: A genetically encoded fluorescent biosensor for extracellular L-lactate.
Authors: Nasu, Y. / Murphy-Royal, C. / Wen, Y. / Haidey, J.N. / Molina, R.S. / Aggarwal, A. / Zhang, S. / Kamijo, Y. / Paquet, M.E. / Podgorski, K. / Drobizhev, M. / Bains, J.S. / Lemieux, M.J. / ...Authors: Nasu, Y. / Murphy-Royal, C. / Wen, Y. / Haidey, J.N. / Molina, R.S. / Aggarwal, A. / Zhang, S. / Kamijo, Y. / Paquet, M.E. / Podgorski, K. / Drobizhev, M. / Bains, J.S. / Lemieux, M.J. / Gordon, G.R. / Campbell, R.E.
History
DepositionMar 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactate-binding periplasmic protein TTHA0766,Lactate-binding periplasmic protein TTHA0766
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1883
Polymers70,0581
Non-polymers1302
Water9,188510
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22780 Å2
Unit cell
Length a, b, c (Å)102.217, 104.983, 138.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-806-

HOH

21A-1198-

HOH

-
Components

#1: Protein Lactate-binding periplasmic protein TTHA0766,Lactate-binding periplasmic protein TTHA0766 / ABC transporter / solute-binding protein / Extracytoplasmic solute receptor protein TTHA0766 / TRAP ...ABC transporter / solute-binding protein / Extracytoplasmic solute receptor protein TTHA0766 / TRAP transporter lactate-binding subunit P


Mass: 70058.258 Da / Num. of mol.: 1 / Mutation: I116N, I138T, K142R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria), (gene. exp.) Thermus thermophilus (bacteria)
Strain: HB8 / Gene: TTHA0766 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SK82
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID / Lactic acid


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium citrate dibasic 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.25→52.492 Å / Num. obs: 35740 / % possible obs: 99.93 % / Redundancy: 5.3 % / CC1/2: 0.986 / Net I/σ(I): 5.75
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 3530 / CC1/2: 0.57

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZZV, 3SG6

2zzv

3sg6


Resolution: 2.25→52.492 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.185 2005 5.61 %
Rwork0.1468 33735 -
obs0.149 35740 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.55 Å2 / Biso mean: 23.4357 Å2 / Biso min: 5.18 Å2
Refinement stepCycle: final / Resolution: 2.25→52.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4511 0 12 510 5033
Biso mean--13.33 28.86 -
Num. residues----564
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.25-2.30630.20211400.15362381
2.3063-2.36870.21541450.15312385
2.3687-2.43840.21111340.14992397
2.4384-2.51710.21171470.15592357
2.5171-2.6070.22951450.14892408
2.607-2.71140.2011370.15142391
2.7114-2.83480.19741420.15712379
2.8348-2.98430.22511400.15842381
2.9843-3.17120.1861490.15172408
3.1712-3.4160.17881370.15222407
3.416-3.75970.17491400.14282418
3.7597-4.30350.16151420.12592439
4.3035-5.42110.1421510.1182441
5.4211-500.17961560.17482543

+
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