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- PDB-6zsm: Crystal structure of rsGCaMP double mutant Ile80His/Val116Ile in ... -

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Basic information

Entry
Database: PDB / ID: 6zsm
TitleCrystal structure of rsGCaMP double mutant Ile80His/Val116Ile in the ON state (non-illuminated)
ComponentsGreen fluorescent protein,Green fluorescent protein,Calmodulin
KeywordsFLUORESCENT PROTEIN / reversible switchable fluorescent protein / calcium sensor / calmodulin
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 / Green fluorescent protein / : / 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 ...Green Fluorescent Protein / Green fluorescent protein / : / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / RCaMP / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Entacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionJul 16, 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: Green fluorescent protein,Green fluorescent protein,Calmodulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,48025
Polymers47,3251
Non-polymers1,15524
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-51 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.540, 121.540, 96.960
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-737-

HOH

21A-773-

HOH

31A-939-

HOH

41A-1000-

HOH

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Components

#1: Protein Green fluorescent protein,Green fluorescent protein,Calmodulin


Mass: 47324.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Entacmaea quadricolor (sea anemone)
Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: K4DIE3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 444 / 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: 3.78 Å3/Da / Density % sol: 67.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 0.20 M sodium formate, 0.1 M Bis-Tris-Propane buffer pH 8.5, 19% (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 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→47.46 Å / Num. obs: 53375 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 41 Å2 / CC1/2: 1 / Net I/σ(I): 22.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3888 / CC1/2: 0.674 / % 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: 6ya9

6ya9


Resolution: 1.95→47.46 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.228 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 2665 5 %RANDOM
Rwork0.1568 ---
obs0.1589 50710 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 920.26 Å2 / Biso mean: 37.825 Å2 / Biso min: 21.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0 Å2
2--0.11 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.95→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 67 444 3678
Biso mean--59.54 48.68 -
Num. residues----399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173047
X-RAY DIFFRACTIONr_angle_refined_deg2.1661.6624460
X-RAY DIFFRACTIONr_angle_other_deg1.5071.5967099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45123.529187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40515601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0261519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023753
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02688
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 193 -
Rwork0.261 3678 -
all-3871 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 2.9928 Å / Origin y: 40.3849 Å / Origin z: 22.504 Å
111213212223313233
T0.0131 Å2-0.0099 Å20.008 Å2-0.0186 Å2-0.0093 Å2--0.0132 Å2
L0.3298 °20.0471 °20.2551 °2-0.017 °2-0.0162 °2--0.4674 °2
S0.0171 Å °0.0421 Å °-0.0032 Å °-0.001 Å °0.0103 Å °0.0045 Å °0.0315 Å °0.0102 Å °-0.0275 Å °

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