[English] 日本語
Yorodumi
- PDB-8a83: rsEGFP2 with a chlorinated chromophore in the fluorescent ON-stat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a83
TitlersEGFP2 with a chlorinated chromophore in the fluorescent ON-state in a crystal dehydrated after illumination
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsFadini, A. / van Thor, J. / Chang, J.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Imperial College LondonPresident's PhD Scholarship United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00752X/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
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 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9515
Polymers28,5671
Non-polymers3844
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-47 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.484, 58.980, 64.484
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: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 109 / 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 % sol: 27.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.76 M ammonium sulfate, 0.1 M HEPES; Cryoprotectant 1.6 M sucrose, 2.72 M ammonium sulfate, 0.16 M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.19 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19 Å / Relative weight: 1
ReflectionResolution: 1.81→38.79 Å / Num. obs: 18434 / % possible obs: 99.54 % / Redundancy: 2 % / CC1/2: 1 / Net I/σ(I): 16.16
Reflection shellResolution: 1.81→1.875 Å / Num. unique obs: 1806 / CC1/2: 0.794

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DTY

5dty


Resolution: 1.81→38.786 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 921 5 %
Rwork0.1998 17486 -
obs0.2013 18407 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.35 Å2 / Biso mean: 34.4947 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 1.81→38.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 20 109 1891
Biso mean--42.31 37.7 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.81-1.90550.32761300.28842469100
1.9055-2.02480.2541280.2356243799
2.0248-2.18120.2371300.20992463100
2.1812-2.40060.24731300.19572471100
2.4006-2.74790.23021310.20042498100
2.7479-3.46180.20641330.20212515100
3.4618-38.7860.22051390.1836263399

+
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