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- PDB-7aug: Crystal structure of rsGCamP1.3 in the ON state -

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Basic information

Entry
Database: PDB / ID: 7aug
TitleCrystal structure of rsGCamP1.3 in the ON state
ComponentsrsGCamP1.3
KeywordsFLUORESCENT PROTEIN / reversible switchable fluorescent protein / calcium sensor / calmodulin
Function / homologyFORMIC ACID
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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: 2022
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
DepositionNov 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 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 1.2Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 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: rsGCamP1.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,20034
Polymers47,6321
Non-polymers1,56833
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-70 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.852, 121.852, 96.416
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-724-

HOH

21A-761-

HOH

31A-871-

HOH

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Components

#1: Protein rsGCamP1.3


Mass: 47632.273 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.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Na Formate, 0.1 M BTP pH 8.5, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 46902 / % possible obs: 99.9 % / Redundancy: 10.6 % / Biso Wilson estimate: 44 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.7
Reflection shellResolution: 2.04→2.16 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 7135 / CC1/2: 0.484

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YA9

6ya9


Resolution: 2.04→47.44 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.507 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2067 2348 5 %RANDOM
Rwork0.1649 ---
obs0.167 44554 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.22 Å2 / Biso mean: 41.528 Å2 / Biso min: 20.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-0 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 2.04→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 95 346 3618
Biso mean--61.74 50.49 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133377
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173158
X-RAY DIFFRACTIONr_angle_refined_deg1.781.6644516
X-RAY DIFFRACTIONr_angle_other_deg1.3841.6017306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8655418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89623.529187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95415608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7241519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023858
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02768
LS refinement shellResolution: 2.04→2.089 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.293 168 -
Rwork0.274 3193 -
obs--99.2 %

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