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- PDB-6tv7: Crystal structure of rsGCaMP in the OFF state (illuminated) -

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Basic information

Entry
Database: PDB / ID: 6tv7
TitleCrystal structure of rsGCaMP in the OFF state (illuminated)
ComponentsrsGCaMP
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: 2.9 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
DepositionJan 9, 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 1.2Jan 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: rsGCaMP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,11410
Polymers47,8391
Non-polymers2759
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-77 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.670, 120.670, 96.020
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-645-

HOH

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Components

#1: Protein rsGCaMP


Mass: 47838.555 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.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 3.65 Å3/Da / Density % sol: 66.33 %
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: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16254 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 55.9 Å2 / CC1/2: 0.996 / Net I/σ(I): 11.17
Reflection shellResolution: 2.9→2.98 Å / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1174 / CC1/2: 0.641

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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: 2.9→47.09 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.904 / SU B: 15.786 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.637 / ESU R Free: 0.341
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 831 5.1 %RANDOM
Rwork0.182 ---
obs0.1855 15423 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 174.87 Å2 / Biso mean: 55.852 Å2 / Biso min: 4.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å2-0 Å2
3----3.22 Å2
Refinement stepCycle: final / Resolution: 2.9→47.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 9 89 3265
Biso mean--46.51 39.3 -
Num. residues----398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133235
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172965
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.6584354
X-RAY DIFFRACTIONr_angle_other_deg1.2721.5936907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4395396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22223.778180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.16815587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3521517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023630
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02657
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 46 -
Rwork0.323 1123 -
all-1169 -
obs--99.91 %

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