[English] 日本語
Yorodumi
- PDB-8ahb: rsEGFP2 photoswitched to its off-state at room temperature and ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ahb
TitlersEGFP2 photoswitched to its off-state at room temperature and back-switched to its on-state at 100K
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / RSFP / Switchable / PTFP / rsEGFP2
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsMantovanelli, A. / Adam, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0047-01 France
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Photophysical Studies at Cryogenic Temperature Reveal a Novel Photoswitching Mechanism of rsEGFP2.
Authors: Mantovanelli, A.M.R. / Glushonkov, O. / Adam, V. / Wulffele, J. / Thedie, D. / Byrdin, M. / Gregor, I. / Nevskyi, O. / Enderlein, J. / Bourgeois, D.
History
DepositionJul 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9165
Polymers28,5321
Non-polymers3844
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-60 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.668, 61.759, 70.445
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Green fluorescent protein /


Mass: 28532.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 100 mM HEPES buffer, pH 8.1 1.9 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 18, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→46.44 Å / Num. obs: 254080 / % possible obs: 99.36 % / Redundancy: 11.8 % / Biso Wilson estimate: 34.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1268 / Rpim(I) all: 0.03823 / Net I/σ(I): 10.87
Reflection shellResolution: 1.79→1.858 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.45 / Num. unique obs: 14673 / CC1/2: 0.237 / CC star: 0.619 / % possible all: 94.43

-
Processing

Software
NameVersionClassification
MxCuBE3data collection
XDSdata reduction
Coot0.9.6model building
MOLREP11.7.03phasing
REFMAC5.8.0267refinement
PHENIX1.20.1_4487refinement
XSCALEdata scaling
pointlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTY

5dty


Resolution: 1.79→46.44 Å / SU ML: 0.3616 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2196 2014 4.98 %
Rwork0.192 38431 -
obs0.1934 40445 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.37 Å2
Refinement stepCycle: LAST / Resolution: 1.79→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1885 0 20 88 1993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061987
X-RAY DIFFRACTIONf_angle_d0.91942695
X-RAY DIFFRACTIONf_chiral_restr0.0574286
X-RAY DIFFRACTIONf_plane_restr0.0062349
X-RAY DIFFRACTIONf_dihedral_angle_d13.4181727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.840.47751310.49392496X-RAY DIFFRACTION90.27
1.84-1.890.40351420.42692749X-RAY DIFFRACTION99.79
1.89-1.940.34471440.36242801X-RAY DIFFRACTION99.73
1.94-2.010.31771450.27982762X-RAY DIFFRACTION99.9
2.01-2.080.30581420.25592769X-RAY DIFFRACTION99.73
2.08-2.160.27281430.23232748X-RAY DIFFRACTION99.86
2.16-2.260.26441440.21062767X-RAY DIFFRACTION99.86
2.26-2.380.22791450.20462763X-RAY DIFFRACTION99.93
2.38-2.530.26881430.18362757X-RAY DIFFRACTION99.9
2.53-2.720.27731470.19262770X-RAY DIFFRACTION100
2.72-30.22541470.19252742X-RAY DIFFRACTION99.93
3-3.430.18981480.16832786X-RAY DIFFRACTION99.9
3.43-4.320.17061470.1522759X-RAY DIFFRACTION99.93
4.33-46.440.17451460.16482762X-RAY DIFFRACTION99.97

+
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