[English] 日本語
Yorodumi
- PDB-6gel: The structure of TWITCH-2B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gel
TitleThe structure of TWITCH-2B
ComponentsGreen fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / Twitch-2B / FRET / Ratiometric Biosensor
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
FORMIC ACID / Green fluorescent protein / Troponin C, skeletal muscle
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Opsanus tau (oyster toadfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsTrigo Mourino, P. / Paulat, M. / Thestrup, T. / Griesbeck, O. / Griesinger, C. / Becker, S.
Citation
Journal: Sci Adv / Year: 2019
Title: Dynamic tuning of FRET in a green fluorescent protein biosensor.
Authors: Trigo-Mourino, P. / Thestrup, T. / Griesbeck, O. / Griesinger, C. / Becker, S.
#1: Journal: Nat. Methods / Year: 2014
Title: Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes.
Authors: Thestrup, T. / Litzlbauer, J. / Bartholomaus, I. / Mues, M. / Russo, L. / Dana, H. / Kovalchuk, Y. / Liang, Y. / Kalamakis, G. / Laukat, Y. / Becker, S. / Witte, G. / Geiger, A. / Allen, T. ...Authors: Thestrup, T. / Litzlbauer, J. / Bartholomaus, I. / Mues, M. / Russo, L. / Dana, H. / Kovalchuk, Y. / Liang, Y. / Kalamakis, G. / Laukat, Y. / Becker, S. / Witte, G. / Geiger, A. / Allen, T. / Rome, L.C. / Chen, T.W. / Kim, D.S. / Garaschuk, O. / Griesinger, C. / Griesbeck, O.
History
DepositionApr 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation_author
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
B: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,95516
Polymers124,9002
Non-polymers1,05514
Water2,036113
1
A: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1038
Polymers62,4501
Non-polymers6537
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,8528
Polymers62,4501
Non-polymers4027
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.075, 156.773, 169.284
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
12A
22B
13A
23B
14A
24A
15A
25B
16A
26B
17A
27B
18A
28B
19A
29B
110B
210B
111B
211B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 64
2010A387 - 446
1020A5 - 65
2020B5 - 65
1030A5 - 64
2030B387 - 446
1040A69 - 172
2040A451 - 554
1050A387 - 446
2050B5 - 64
1060A69 - 447
2060B69 - 447
1070A69 - 172
2070B451 - 554
1080A451 - 554
2080B69 - 172
1090A451 - 555
2090B451 - 555
10100B5 - 64
20100B387 - 446
10110B69 - 172
20110B451 - 554

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein


Mass: 62449.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Opsanus tau (oyster toadfish)
Gene: GFP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212, UniProt: W5IDB2

-
Non-polymers , 5 types, 127 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M sodium formiate, 5 mM calcium chloride, 18 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→47.93 Å / Num. obs: 50452 / % possible obs: 98.69 % / Redundancy: 6.62 % / Rrim(I) all: 0.033 / Net I/σ(I): 24.16
Reflection shellResolution: 2.51→2.61 Å / Redundancy: 6.31 % / Mean I/σ(I) obs: 3.32 / Rrim(I) all: 0.241

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SADABSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.51→47.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 18.248 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / ESU R Free: 0.255
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 2656 5 %RANDOM
Rwork0.1953 ---
obs0.1975 50452 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 131.61 Å2 / Biso mean: 62.652 Å2 / Biso min: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.18 Å2-0 Å2
3----2.7 Å2
Refinement stepCycle: final / Resolution: 2.51→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8486 0 45 113 8644
Biso mean--67.54 45.6 -
Num. residues----1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0148779
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177759
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.67411792
X-RAY DIFFRACTIONr_angle_other_deg1.0291.6618206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.24151057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74524.108482
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.371151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7561537
X-RAY DIFFRACTIONr_chiral_restr0.0960.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029839
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021637
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A14300.13
12A14300.13
21A15710.1
22B15710.1
31A14100.14
32B14100.14
41A28070.1
42A28070.1
51A14740.12
52B14740.12
61A105100.1
62B105100.1
71A27610.11
72B27610.11
81A28100.12
82B28100.12
91A31010.06
92B31010.06
101B14460.13
102B14460.13
111B27380.12
112B27380.12
LS refinement shellResolution: 2.51→2.575 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 158 -
Rwork0.285 3484 -
all-3642 -
obs--93.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8014-1.049-0.11683.4475-0.00221.0899-0.14860.0171-0.22340.27160.13720.1640.18690.1720.01150.3276-0.02560.11030.058-0.03710.0944.07480.76581.541
20.91660.0606-1.34520.77950.37373.8231-0.10860.28190.1189-0.1280.0601-0.02840.0496-0.19080.04850.3127-0.1526-0.11010.1560.1010.091618.366119.8247.464
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 555
2X-RAY DIFFRACTION2B5 - 555

+
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