[English] 日本語
Yorodumi
- PDB-8a6s: Room temperature rsEGFP2 with a chlorinated chromophore 1 microse... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a6s
TitleRoom temperature rsEGFP2 with a chlorinated chromophore 1 microsecond after Photoexcitation
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP-like protein / beta-barrel / bioluminescence
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsFadini, A. / van Thor, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Imperial College LondonPresident's PhD Scholarship United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00752X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism.
Authors: Fadini, A. / Hutchison, C.D.M. / Morozov, D. / Chang, J. / Maghlaoui, K. / Perrett, S. / Luo, F. / Kho, J.C.X. / Romei, M.G. / Morgan, R.M.L. / Orr, C.M. / Cordon-Preciado, V. / Fujiwara, T. ...Authors: Fadini, A. / Hutchison, C.D.M. / Morozov, D. / Chang, J. / Maghlaoui, K. / Perrett, S. / Luo, F. / Kho, J.C.X. / Romei, M.G. / Morgan, R.M.L. / Orr, C.M. / Cordon-Preciado, V. / Fujiwara, T. / Nuemket, N. / Tosha, T. / Tanaka, R. / Owada, S. / Tono, K. / Iwata, S. / Boxer, S.G. / Groenhof, G. / Nango, E. / van Thor, J.J.
History
DepositionJun 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 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


Theoretical massNumber of molelcules
Total (without water)28,5671
Polymers28,5671
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.990, 62.910, 72.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Green fluorescent protein /


Mass: 28566.648 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 1.3M ammonium sulfate, 100mM Hepes pH 8.1, 20mM NaCl

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.18 Å
DetectorType: MPCCD / Detector: CCD / Date: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 1.63→31.46 Å / Num. obs: 30206 / % possible obs: 100 % / Redundancy: 328.7 % / CC1/2: 0.98 / Net I/σ(I): 6.183
Reflection shellResolution: 1.63→1.688 Å / Num. unique obs: 2952 / CC1/2: 0.47
Serial crystallography sample deliveryMethod: injection

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PFT

6pft


Resolution: 1.63→31.455 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.44 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 1510 5.01 %
Rwork0.1685 28633 -
obs0.1701 30143 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.08 Å2 / Biso mean: 28.5123 Å2 / Biso min: 14.15 Å2
Refinement stepCycle: final / Resolution: 1.63→31.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1884 0 600 125 2609
Biso mean--27.77 36.75 -
Num. residues----164
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.63-1.68260.31761330.32192567
1.6826-1.74270.32861440.2822555
1.7427-1.81250.26831360.24842579
1.8125-1.8950.24341370.20552538
1.895-1.99490.20731410.18482580
1.9949-2.11980.21541280.1742581
2.1198-2.28350.23371440.16512581
2.2835-2.51320.21511280.16832614
2.5132-2.87660.22661500.16812612
2.8766-3.62340.18741200.14632659
3.6234-31.4550.15561490.14642767

+
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