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- PDB-6ya9: Crystal structure of rsGCaMP in the ON state (non-illuminated) -

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Basic information

Entry
Database: PDB / ID: 6ya9
TitleCrystal structure of rsGCaMP in the ON state (non-illuminated)
ComponentsrsCGaMP
KeywordsFLUORESCENT PROTEIN / reversible switchable fluorescent protein / calcium sensor / calmodulin
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJanowski, R. / Fuenzalida-Werner, J.P. / Mishra, K. / Stiel, A.C. / Niessing, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)STI 656/1-1 Germany
CitationJournal: Nat.Biotechnol. / Year: 2021
Title: Genetically encoded photo-switchable molecular sensors for optoacoustic and super-resolution imaging.
Authors: Mishra, K. / Fuenzalida-Werner, J.P. / Pennacchietti, F. / Janowski, R. / Chmyrov, A. / Huang, Y. / Zakian, C. / Klemm, U. / Testa, I. / Niessing, D. / Ntziachristos, V. / Stiel, A.C.
History
DepositionMar 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: rsCGaMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5678
Polymers47,2861
Non-polymers2817
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-73 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.430, 119.430, 96.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-729-

HOH

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Components

#1: Protein rsCGaMP


Mass: 47285.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.21 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000029 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000029 Å / Relative weight: 1
ReflectionResolution: 2.15→44.82 Å / Num. obs: 38514 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.2 % / Biso Wilson estimate: 52 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 2.15→2.2 Å / Redundancy: 15 % / Num. unique obs: 2816 / CC1/2: 0.746 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK4

3ek4


Resolution: 2.15→44.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.945 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.155
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1828 4.7 %RANDOM
Rwork0.1868 ---
obs0.1889 36685 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 167.22 Å2 / Biso mean: 52.208 Å2 / Biso min: 29.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å2-0 Å20 Å2
2--0.35 Å20 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 2.15→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3190 0 7 233 3430
Biso mean--67.5 54.22 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133261
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172979
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.6574391
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5936942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06123.846182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.16215591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9111517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023666
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02661
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 122 -
Rwork0.274 2686 -
all-2808 -
obs--99.96 %

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