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- PDB-4ik5: High resolution structure of Delta-REST-GCaMP3 -

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Basic information

Entry
Database: PDB / ID: 4ik5
TitleHigh resolution structure of Delta-REST-GCaMP3
ComponentsRCaMP, Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / calcium indicator / mutants / fluorescent intensity / dimerization / beta-barrel / Calmodulin
Function / homology
Function and homology information


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 / EF-hand calcium-binding domain. ...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
RCaMP / Green fluorescent protein
Similarity search - Component
Biological speciesEntacmaea quadricolor (sea anemone)
Aequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, Y. / Song, X. / Miao, L. / Zhu, Y. / Ji, G.
CitationJournal: Protein Cell / Year: 2013
Title: Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement.
Authors: Chen, Y. / Song, X. / Ye, S. / Miao, L. / Zhu, Y. / Zhang, R.G. / Ji, G.
History
DepositionDec 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_conn / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _struct_ref.pdbx_align_begin ..._entity.pdbx_mutation / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RCaMP, Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9255
Polymers46,7641
Non-polymers1604
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.021, 120.021, 96.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-708-

HOH

21A-869-

HOH

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Components

#1: Protein RCaMP, Green fluorescent protein


Mass: 46764.324 Da / Num. of mol.: 1
Mutation: M153K, V163A, S175G, D180Y, T203V, A206K, H231L, F64L, V93I, I354T
Source method: isolated from a genetically manipulated source
Details: CHIMERA OF RESIDUES 25-48 OF RCaMP, LINKER LE, RESIDUES 149-238 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 2-144 OF GREEN FLUORESCENT PROTEIN, RESIDUES 284-432 OF RCaMP
Source: (gene. exp.) Entacmaea quadricolor (sea anemone), (gene. exp.) Aequorea victoria (jellyfish)
Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: K4DIE3, UniProt: P42212
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Sequence details(1) THIS CHIMERA COMPRISES OF RESIDUES 25-48 OF RCaMP, LINKER LE, RESIDUES 149-238 OF GREEN ...(1) THIS CHIMERA COMPRISES OF RESIDUES 25-48 OF RCaMP, LINKER LE, RESIDUES 149-238 OF GREEN FLUORESCENT PROTEIN, LINKER GGTGGSMV, RESIDUES 2-144 OF GREEN FLUORESCENT PROTEIN, RESIDUES 284-432 OF RCaMP (2) RESIDUE SER 222 HAS BEEN MUTATED TO GLY. RESIDUES GLY 222, TYR 223 AND GLY 224 CONSTITUTE THE CHROMOPHORE CRO 222

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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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris pH 8.5, NH4OAc, 23% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 3, 2012
RadiationMonochromator: Be filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→46.95 Å / Num. all: 28413 / Num. obs: 27021 / % possible obs: 95.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.4→2.47 Å / % possible all: 47.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.655 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22797 1244 5 %RANDOM
Rwork0.17586 ---
all0.1843 23790 --
obs0.17846 23529 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 4 306 3433
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.023
X-RAY DIFFRACTIONr_angle_refined_deg1.998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 84 -
Rwork0.23 1702 -
obs--98.51 %

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