[English] 日本語
Yorodumi
- PDB-7qll: rsKiiro Thermal annealing at 290K of 200K Cis intermediate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qll
TitlersKiiro Thermal annealing at 290K of 200K Cis intermediate
ComponentsrsKiiro
KeywordsFLUORESCENT PROTEIN / rsKiiro
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green to red photoconvertible GFP-like protein EosFP
Function and homology information
Biological speciesLobophyllia hemprichii (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.324 Å
Authorsvan Thor, J.J. / Baxter, J.M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00752X/1 United Kingdom
CitationJournal: Nat.Chem. / Year: 2023
Title: Optical control of ultrafast structural dynamics in a fluorescent protein.
Authors: Hutchison, C.D.M. / Baxter, J.M. / Fitzpatrick, A. / Dorlhiac, G. / Fadini, A. / Perrett, S. / Maghlaoui, K. / Lefevre, S.B. / Cordon-Preciado, V. / Ferreira, J.L. / Chukhutsina, V.U. / ...Authors: Hutchison, C.D.M. / Baxter, J.M. / Fitzpatrick, A. / Dorlhiac, G. / Fadini, A. / Perrett, S. / Maghlaoui, K. / Lefevre, S.B. / Cordon-Preciado, V. / Ferreira, J.L. / Chukhutsina, V.U. / Garratt, D. / Barnard, J. / Galinis, G. / Glencross, F. / Morgan, R.M. / Stockton, S. / Taylor, B. / Yuan, L. / Romei, M.G. / Lin, C.Y. / Marangos, J.P. / Schmidt, M. / Chatrchyan, V. / Buckup, T. / Morozov, D. / Park, J. / Park, S. / Eom, I. / Kim, M. / Jang, D. / Choi, H. / Hyun, H. / Park, G. / Nango, E. / Tanaka, R. / Owada, S. / Tono, K. / DePonte, D.P. / Carbajo, S. / Seaberg, M. / Aquila, A. / Boutet, S. / Barty, A. / Iwata, S. / Boxer, S.G. / Groenhof, G. / van Thor, J.J.
History
DepositionDec 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Aug 23, 2023Group: Database references / Structure summary / Category: citation / citation_author / entity_name_com
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / citation
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: rsKiiro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3413
Polymers25,1521
Non-polymers1882
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-3 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.671, 73.803, 78.111
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein rsKiiro / Green to red photoconvertible GFP-like protein EosFP / rsKiiro


Mass: 25152.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lobophyllia hemprichii (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5S6Z9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 8.4
Details: 0.2 M LITHIUM SULFATE 0.1 M TRIS-CL PH 8.5 23-30% PEG 3350,

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.72932 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.72932 Å / Relative weight: 1
ReflectionResolution: 1.324→53.703 Å / Num. obs: 44562 / % possible obs: 86.3 % / Redundancy: 15.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.026 / Net I/σ(I): 15.7
Reflection shellResolution: 1.336→1.4 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2224 / CC1/2: 0.455

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OQ9

5oq9


Resolution: 1.324→53.703 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.173 / SU B: 1.011 / SU ML: 0.039 / Average fsc free: 0.9265 / Average fsc work: 0.9333 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.063
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1976 2261 5.074 %
Rwork0.1695 42301 -
all0.171 --
obs-44562 84.302 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.881 Å2
Baniso -1Baniso -2Baniso -3
1-0.086 Å20 Å20 Å2
2---0.005 Å20 Å2
3----0.081 Å2
Refinement stepCycle: LAST / Resolution: 1.324→53.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 11 177 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131983
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161827
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.6842696
X-RAY DIFFRACTIONr_angle_other_deg1.5071.6054254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5325256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55622.991107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.64515351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8451510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022310
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02467
X-RAY DIFFRACTIONr_nbd_refined0.2610.2316
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21653
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2854
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0270.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2680.219
X-RAY DIFFRACTIONr_nbd_other0.2540.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4190.216
X-RAY DIFFRACTIONr_mcbond_it1.6431.494946
X-RAY DIFFRACTIONr_mcbond_other1.621.482944
X-RAY DIFFRACTIONr_mcangle_it2.5352.2131201
X-RAY DIFFRACTIONr_mcangle_other2.5242.2141201
X-RAY DIFFRACTIONr_scbond_it2.7531.7861037
X-RAY DIFFRACTIONr_scbond_other2.7531.7861037
X-RAY DIFFRACTIONr_scangle_it4.192.5521486
X-RAY DIFFRACTIONr_scangle_other4.1852.5531486
X-RAY DIFFRACTIONr_lrange_it5.61717.4882114
X-RAY DIFFRACTIONr_lrange_other5.61717.5082114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.324-1.3580.274220.324569X-RAY DIFFRACTION15.3946
1.358-1.3960.289670.3121464X-RAY DIFFRACTION40.7398
1.396-1.4360.3141210.2942106X-RAY DIFFRACTION60.9469
1.436-1.480.3321430.2772559X-RAY DIFFRACTION75.7924
1.48-1.5290.2371620.2392848X-RAY DIFFRACTION87.4238
1.529-1.5820.2171380.2083108X-RAY DIFFRACTION97.6534
1.582-1.6420.2151420.1813076X-RAY DIFFRACTION99.321
1.642-1.7090.2071470.1592964X-RAY DIFFRACTION100
1.709-1.7850.1911600.1542840X-RAY DIFFRACTION100
1.785-1.8720.1871420.1572691X-RAY DIFFRACTION100
1.872-1.9730.1961600.1542580X-RAY DIFFRACTION100
1.973-2.0930.1881450.1482445X-RAY DIFFRACTION100
2.093-2.2370.1781430.1412317X-RAY DIFFRACTION100
2.237-2.4160.1741160.1492154X-RAY DIFFRACTION100
2.416-2.6470.1651090.1481994X-RAY DIFFRACTION100
2.647-2.9590.172980.1451816X-RAY DIFFRACTION100
2.959-3.4160.168820.1531623X-RAY DIFFRACTION100
3.416-4.1810.187720.1561390X-RAY DIFFRACTION100
4.181-5.9050.19530.191105X-RAY DIFFRACTION100
5.905-53.7030.351390.253652X-RAY DIFFRACTION100

+
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://pdbjlc1.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