[English] 日本語
Yorodumi
- PDB-3e5w: Crystal Structure Analysis of FP611 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e5w
TitleCrystal Structure Analysis of FP611
ComponentsRed fluorescent protein eqFP611
KeywordsFLUORESCENT PROTEIN / Chromophore / Luminescence / Photoprotein / RFP639 / eqFP611 / cis trans isomer / red fluorescent protein
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.71 Å
AuthorsNienhaus, K. / Nar, H. / Heilker, R. / Wiedenmann, J. / Nienhaus, G.U.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Trans-cis isomerization is responsible for the red-shifted fluorescence in variants of the red fluorescent protein eqFP611.
Authors: Nienhaus, K. / Nar, H. / Heilker, R. / Wiedenmann, J. / Nienhaus, G.U.
History
DepositionAug 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: 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 1.4Aug 30, 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: Red fluorescent protein eqFP611
B: Red fluorescent protein eqFP611
C: Red fluorescent protein eqFP611
D: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)110,7904
Polymers110,7904
Non-polymers00
Water20,1231117
1
A: Red fluorescent protein eqFP611
D: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)55,3952
Polymers55,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-17 kcal/mol
Surface area18380 Å2
MethodPISA
2
B: Red fluorescent protein eqFP611
C: Red fluorescent protein eqFP611


Theoretical massNumber of molelcules
Total (without water)55,3952
Polymers55,3952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-17 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.250, 104.460, 133.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Red fluorescent protein eqFP611 / GFP-like chromoprotein / FP611


Mass: 27697.598 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone)
Description: synonymous source organism name Parasicyonis actinostoloides
Production host: Escherichia coli (E. coli) / Strain (production host): M15pREP4 / References: UniProt: Q8ISF8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1117 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 8000, pH 4.6, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.96 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.71→62.8 Å / Num. all: 106391 / Num. obs: 106080 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 26.71 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.8
Reflection shellResolution: 1.71→1.78 Å / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.9 / Num. measured obs: 80783 / Num. unique obs: 11797 / % possible all: 97.4

-
Processing

Software
NameVersionClassificationNB
XSCALEdata processing
TNTrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER-TNT2.1.1refinement
RefinementStarting model: 1UIS

1uis


Resolution: 1.71→62.8 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4986 4.7 %RANDOM
Rwork0.183 ---
all0.186 106391 --
obs0.184 106079 98.06 %-
Displacement parametersBiso max: 91.8 Å2 / Biso mean: 25.702 Å2 / Biso min: 10.78 Å2
Baniso -1Baniso -2Baniso -3
1-4.088 Å20 Å20 Å2
2---9.403 Å20 Å2
3---5.315 Å2
Refinement stepCycle: LAST / Resolution: 1.71→62.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7252 0 0 1117 8369
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00474402
X-RAY DIFFRACTIONt_angle_deg0.91699682
X-RAY DIFFRACTIONt_dihedral_angle_d18.25914920
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0051762
X-RAY DIFFRACTIONt_gen_planes0.01510885
X-RAY DIFFRACTIONt_it1.014744020
X-RAY DIFFRACTIONt_nbd0.02605
LS refinement shellResolution: 1.71→1.81 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.248 784 4.7 %
Rwork0.226 15889 -
all0.227 16673 -
obs--98.06 %

+
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