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- PDB-6gez: THE STRUCTURE OF TWITCH-2B N532F -

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Basic information

Entry
Database: PDB / ID: 6gez
TitleTHE STRUCTURE OF TWITCH-2B N532F
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
: / 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. ...: / 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 / MOLECULAR REPLACEMENT / Resolution: 2.47 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 27, 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 / citation_author / Item: _citation.title
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 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)125,35611
Polymers124,9662
Non-polymers3909
Water1,40578
1
A: Green fluorescent protein,Optimized Ratiometric Calcium Sensor,Green fluorescent protein,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7477
Polymers62,4831
Non-polymers2646
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)62,6094
Polymers62,4831
Non-polymers1263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.619, 157.472, 169.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 62482.961 Da / Num. of mol.: 2 / Mutation: N532F
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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.2 M SODIUM FORMIATE, PH 7.0, 5 MM CALCIUM CHLORIDE, 20 % PEG3350

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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: Oct 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.47→115.34 Å / Num. obs: 54945 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 6.36 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.95
Reflection shellResolution: 2.47→2.57 Å / Redundancy: 5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.95 / % possible all: 80.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GEL

6gel


Resolution: 2.47→115.34 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.885 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2736 5 %RANDOM
Rwork0.2067 ---
obs0.208 51921 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 144.05 Å2 / Biso mean: 72.324 Å2 / Biso min: 39.62 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2---0.15 Å20 Å2
3----2.37 Å2
Refinement stepCycle: final / Resolution: 2.47→115.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8531 0 19 78 8628
Biso mean--75.47 55.17 -
Num. residues----1067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0198818
X-RAY DIFFRACTIONr_bond_other_d0.0050.028222
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.96911894
X-RAY DIFFRACTIONr_angle_other_deg1.249318993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.29851071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68425.278449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.871151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3941537
X-RAY DIFFRACTIONr_chiral_restr0.0910.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210073
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022028
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.472→2.536 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 147 -
Rwork0.378 2792 -
all-2939 -
obs--71.58 %
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)
10.72130.4848-0.06952.7943-0.27260.9234-0.03630.01740.1498-0.11280.06910.1069-0.03630.0535-0.03280.30130.0355-0.08680.0117-0.00880.0533-24.562-2.4682.953
20.48230.18291.10260.70380.25043.1075-0.0732-0.1479-0.06820.02810.0574-0.0786-0.0115-0.11660.01580.28690.16520.10540.20340.07850.1071-10.461-41.45837.393
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 555
2X-RAY DIFFRACTION2B5 - 555

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