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- PDB-7st4: Calcium-saturated jGCaMP8.410.80 -

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Basic information

Entry
Database: PDB / ID: 7st4
TitleCalcium-saturated jGCaMP8.410.80
ComponentsjGCaMP8.410.80
KeywordsFLUORESCENT PROTEIN / GCaMP / genetically encoded Calcium indicator
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y. / Looger, L.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2023
Title: Fast and sensitive GCaMP calcium indicators for imaging neural populations
Authors: Zhang, Y. / Rozsa, M. / Liang, Y. / Bushey, D. / Wei, Z. / Zheng, J. / Reep, D. / Broussard, G.J. / Tsang, A. / Tsegaye, G. / Narayan, S. / Obara, C.J. / Lim, J.X. / Patel, R. / Zhang, R. / ...Authors: Zhang, Y. / Rozsa, M. / Liang, Y. / Bushey, D. / Wei, Z. / Zheng, J. / Reep, D. / Broussard, G.J. / Tsang, A. / Tsegaye, G. / Narayan, S. / Obara, C.J. / Lim, J.X. / Patel, R. / Zhang, R. / Ahrens, M.B. / Turner, G.C. / Wang, S.S.H. / Korff, W.L. / Schreiter, E.R. / Svoboda, K. / Hasseman, J.P. / Kolb, I. / Looger, L.L.
History
DepositionNov 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: jGCaMP8.410.80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9417
Polymers47,5381
Non-polymers4026
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.597, 120.597, 97.876
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-701-

HOH

21A-836-

HOH

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Components

#1: Protein jGCaMP8.410.80


Mass: 47538.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CRO is PEPTIDE (thr-tyr-gly) DERIVED CHROMOPHORE / Source: (gene. exp.) synthetic construct (others) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.7 Å3/Da / Density % sol: 67.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 3350, potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→47.24 Å / Num. obs: 49292 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.06 / Net I/σ(I): 31.3 / Num. measured all: 707051
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.0512.90.5144616035830.9490.1480.5355.6100
8.94-47.2411.70.029755364310.0090.0371.798.7

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EK4

3ek4


Resolution: 2→45.39 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.487 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 2378 4.8 %RANDOM
Rwork0.1751 ---
obs0.1762 46851 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.53 Å2 / Biso mean: 33.248 Å2 / Biso min: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 2→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 20 243 3236
Biso mean--54.28 39.89 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133074
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162841
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.6474160
X-RAY DIFFRACTIONr_angle_other_deg1.4921.5896542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96323.935155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81415512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3471511
X-RAY DIFFRACTIONr_chiral_restr0.0850.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02674
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 193 -
Rwork0.209 3381 -
all-3574 -
obs--99.97 %

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