[English] 日本語
Yorodumi
- PDB-5fhv: Crystal structure of mCherry after reaction with 2-mercaptoethanol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fhv
TitleCrystal structure of mCherry after reaction with 2-mercaptoethanol
ComponentsmCherry-BME
KeywordsFLUORESCENT PROTEIN / 2-mercaptoethanol / Michael addition
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / metal ion binding
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / TRIETHYLENE GLYCOL / mOrange
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsDe Zitter, E. / Dedecker, P. / Van Meervelt, L.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Efficient switching of mCherry fluorescence using chemical caging.
Authors: Cloin, B.M.C. / De Zitter, E. / Salas, D. / Gielen, V. / Folkers, G.E. / Mikhaylova, M. / Bergeler, M. / Krajnik, B. / Harvey, J. / Hoogenraad, C.C. / Van Meervelt, L. / Dedecker, P. / Kapitein, L.C.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mCherry-BME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1566
Polymers30,4891
Non-polymers6675
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint2 kcal/mol
Surface area10370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.783, 43.244, 61.234
Angle α, β, γ (deg.)90.000, 111.520, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein mCherry-BME


Mass: 30489.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): JM109 / References: UniProt: D0VWW2*PLUS
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M MgCl2.6H2O, 0.1 M Tris pH 8.5, 25 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→45.381 Å / Num. obs: 34495 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 13.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.5830.5622.1199
8.49-45.383.30.01846.4198.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.65 Å45.38 Å
Translation5.65 Å45.38 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSJanuary 22, 2015data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q

2h5q


Resolution: 1.55→45.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1876 1708 4.95 %Random selection
Rwork0.1567 32769 --
obs0.1583 34477 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.86 Å2 / Biso mean: 17.7512 Å2 / Biso min: 5.7 Å2
Refinement stepCycle: final / Resolution: 1.55→45.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 41 315 2153
Biso mean--35.94 29.13 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062034
X-RAY DIFFRACTIONf_angle_d1.3252745
X-RAY DIFFRACTIONf_chiral_restr0.043263
X-RAY DIFFRACTIONf_plane_restr0.005362
X-RAY DIFFRACTIONf_dihedral_angle_d13.417790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.59560.27631450.23442670281598
1.5956-1.64710.24871310.21452688281999
1.6471-1.7060.23471350.20322732286799
1.706-1.77430.20311350.19292696283199
1.7743-1.85510.22481410.17412716285799
1.8551-1.95290.20531590.17072714287399
1.9529-2.07520.19161220.154227382860100
2.0752-2.23540.17991400.147827502890100
2.2354-2.46040.19241380.159327462884100
2.4604-2.81640.17071390.153427462885100
2.8164-3.54810.19661520.138127682920100
3.5481-45.40050.15311710.13522805297699

+
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