[English] 日本語
Yorodumi
- PDB-6dej: The structure of HcRed7, a brighter and red-shifted HcRed variant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dej
TitleThe structure of HcRed7, a brighter and red-shifted HcRed variant
ComponentsGFP-like non-fluorescent chromoprotein
KeywordsFLUORESCENT PROTEIN / HcRed / red / far-red
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / GFP-like non-fluorescent chromoprotein
Function and homology information
Biological speciesHeteractis crispa (leathery sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6279 Å
AuthorsWannier, T.M. / Mayo, S.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)R21EB018579 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Monomerization of far-red fluorescent proteins.
Authors: Wannier, T.M. / Gillespie, S.K. / Hutchins, N. / McIsaac, R.S. / Wu, S.Y. / Shen, Y. / Campbell, R.E. / Brown, K.S. / Mayo, S.L.
History
DepositionMay 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GFP-like non-fluorescent chromoprotein
B: GFP-like non-fluorescent chromoprotein
C: GFP-like non-fluorescent chromoprotein
D: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1088
Polymers107,3344
Non-polymers7744
Water16,952941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Analytical Ultracentrifugation and Size Exclusion Chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-54 kcal/mol
Surface area33200 Å2
2
A: GFP-like non-fluorescent chromoprotein
B: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3104
Polymers53,6672
Non-polymers6432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-28 kcal/mol
Surface area18420 Å2
MethodPISA
3
C: GFP-like non-fluorescent chromoprotein
D: GFP-like non-fluorescent chromoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7984
Polymers53,6672
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.342, 122.057, 75.254
Angle α, β, γ (deg.)90.000, 108.750, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

-
Components

#1: Protein
GFP-like non-fluorescent chromoprotein / HcRed / hcCP


Mass: 26833.428 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Heteractis crispa (leathery sea anemone)
Production host: Escherichia coli (E. coli) / References: UniProt: Q95W85
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 941 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 12 mg/ml protein 0.2 M ammonium sulfate 0.1 M bis-tris pH 6.5 25 w/v polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6279→39.3 Å / Num. obs: 111329 / % possible obs: 95.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.6
Reflection shellResolution: 1.628→1.72 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.554 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 13784 / % possible all: 79.7

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
Web-Icedata collection
Cootmodel building
RefinementResolution: 1.6279→33.6822 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.214 5487 5 %
Rwork0.178 --
obs-111112 95.9 %
Displacement parametersBiso mean: 31.96 Å2
Refinement stepCycle: LAST / Resolution: 1.6279→33.6822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 42 941 8150
LS refinement shellResolution: 1.6279→1.6464 Å
RfactorNum. reflection% reflection
Rfree0.4188 111 5 %
Rwork0.4073 1721 -
obs--47.3 %

+
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://pdbjlvh1.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