[English] 日本語
Yorodumi
- PDB-2yfp: STRUCTURE OF YELLOW-EMISSION VARIANT OF GFP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yfp
TitleSTRUCTURE OF YELLOW-EMISSION VARIANT OF GFP
ComponentsPROTEIN (GREEN FLUORESCENT PROTEIN)
KeywordsPHOTOSYNTHESIS / GREEN FLUORESCENT PROTEIN / YELLOW-EMISSION VARIANT / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
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
Green fluorescent protein / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWachter, R.M. / Elsliger, M.A. / Kallio, K. / Hanson, G.T. / Remington, S.J.
CitationJournal: Structure / Year: 1998
Title: Structural basis of spectral shifts in the yellow-emission variants of green fluorescent protein.
Authors: Wachter, R.M. / Elsliger, M.A. / Kallio, K. / Hanson, G.T. / Remington, S.J.
History
DepositionAug 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (GREEN FLUORESCENT PROTEIN)


Theoretical massNumber of molelcules
Total (without water)26,8801
Polymers26,8801
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.994, 62.756, 69.929
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (GREEN FLUORESCENT PROTEIN)


Mass: 26880.330 Da / Num. of mol.: 1 / Mutation: S65G,V68L,S72A,T203Y,H148G,Q80R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Plasmid: PRSETB (INVITROGEN) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: Q93125, UniProt: P42212*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FLUOROPHORE (PBI) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF ...THE FLUOROPHORE (PBI) IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF SER 65, HIS 66, GLY 67. RESIDUES 65, 66, AND 67 ARE NOT PRESENT IN THE ENTRY AND ARE INSTEAD REPLACED WITH PBI 66.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.7 % / Description: ISOMORPHOUS REPLACEMENT
Crystal growpH: 4.6 / Details: pH 4.6
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
250 mMHEPES1drop
32.2 Msodium potassium phosphate1reservoir

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Dec 5, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→24 Å / Num. obs: 7373 / % possible obs: 99 % / Observed criterion σ(I): 1.9 / Redundancy: 4.1 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.23
Reflection shellResolution: 2.6→2.78 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 2.24 / % possible all: 97
Reflection
*PLUS
Num. measured all: 29904
Reflection shell
*PLUS
% possible obs: 97 %

-
Processing

Software
NameClassification
TNTrefinement
DATACdata reduction
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 2.6→24 Å / Isotropic thermal model: TNT / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.161 --
all0.161 7301 -
obs-7301 98 %
Solvent computationBsol: 147 Å2 / ksol: 0.712 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 0 30 1777
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0118541.5
X-RAY DIFFRACTIONt_angle_deg1.9224973
X-RAY DIFFRACTIONt_dihedral_angle_d20.5110840
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.008522
X-RAY DIFFRACTIONt_gen_planes0.0162656
X-RAY DIFFRACTIONt_it3.1118292.5
X-RAY DIFFRACTIONt_nbd0.0233310
Software
*PLUS
Name: TNT / Version: 5F / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.510
X-RAY DIFFRACTIONt_plane_restr0.0166

+
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