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- PDB-6gel: The structure of TWITCH-2B -

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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


myosin II complex / bioluminescence / generation of precursor metabolites and energy / calcium ion binding
Similarity search - Function
EF-hand / : / Green fluorescent protein, GFP / Recoverin; domain 1 / 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 / : / Green fluorescent protein, GFP / Recoverin; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
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
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTHRTHRAA5 - 645 - 64
21GLYGLYTHRTHRAA387 - 446385 - 444
12GLYGLYLEULEUAA5 - 655 - 65
22GLYGLYLEULEUBB5 - 655 - 65
13GLYGLYTHRTHRAA5 - 645 - 64
23GLYGLYTHRTHRBB387 - 446385 - 444
14VALVALILEILEAA69 - 17267 - 170
24LEULEUILEILEAA451 - 554447 - 550
15GLYGLYTHRTHRAA387 - 446385 - 444
25GLYGLYTHRTHRBB5 - 645 - 64
16VALVALLEULEUAA69 - 44767 - 445
26VALVALLEULEUBB69 - 44767 - 445
17VALVALILEILEAA69 - 17267 - 170
27LEULEUILEILEBB451 - 554447 - 550
18LEULEUILEILEAA451 - 554447 - 550
28VALVALILEILEBB69 - 17267 - 170
19LEULEUGLUGLUAA451 - 555447 - 551
29LEULEUGLUGLUBB451 - 555447 - 551
110GLYGLYTHRTHRBB5 - 645 - 64
210GLYGLYTHRTHRBB387 - 446385 - 444
111VALVALILEILEBB69 - 17267 - 170
211LEULEUILEILEBB451 - 554447 - 550

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

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Components

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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

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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


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


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


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


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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