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- PDB-8am4: Cl-rsEGFP2 Long Wavelength Structure -

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Basic information

Entry
Database: PDB / ID: 8am4
TitleCl-rsEGFP2 Long Wavelength Structure
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP-like protein / beta-barrel / bioluminescence
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsOrr, C.M. / Fadini, A. / van Thor, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Imperial College LondonPresident's PhD Scholarship United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P00752X/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism.
Authors: Fadini, A. / Hutchison, C.D.M. / Morozov, D. / Chang, J. / Maghlaoui, K. / Perrett, S. / Luo, F. / Kho, J.C.X. / Romei, M.G. / Morgan, R.M.L. / Orr, C.M. / Cordon-Preciado, V. / Fujiwara, T. ...Authors: Fadini, A. / Hutchison, C.D.M. / Morozov, D. / Chang, J. / Maghlaoui, K. / Perrett, S. / Luo, F. / Kho, J.C.X. / Romei, M.G. / Morgan, R.M.L. / Orr, C.M. / Cordon-Preciado, V. / Fujiwara, T. / Nuemket, N. / Tosha, T. / Tanaka, R. / Owada, S. / Tono, K. / Iwata, S. / Boxer, S.G. / Groenhof, G. / Nango, E. / van Thor, J.J.
History
DepositionAug 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,5671
Polymers28,5671
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.915, 63.25, 70.587
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Green fluorescent protein /


Mass: 28566.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212
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: 2.18 Å3/Da / Density % sol: 43.54 % / Description: 500 um x 200 um x 200 um
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Hepes pH 8.0, 1.80 M ammonium sulphate, 20 mM NaCl

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
150Conductive cooling1N
250Conductive cooling1N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2313.0996
SYNCHROTRONDiamond I2324.42801
Detector
TypeIDDetectorDate
DECTRIS PILATUS 12M1PIXELJul 8, 2021
DECTRIS PILATUS 12M2PIXELJul 8, 2021
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111SINGLE WAVELENGTHMx-ray1
2Si111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
13.09961
24.428011
Reflection

Entry-ID: 8AM4

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)Biso Wilson estimate (Å2)
2.02-47.111229780.71.90.9980.0320.0320.046124.7
2.89-50.92477688.76.20.9870.0521336.36
Reflection shellResolution: 2.02→2.08 Å / Rmerge(I) obs: 0.112 / Num. unique obs: 571 / CC1/2: 0.987 / Rpim(I) all: 0.112 / Rrim(I) all: 0.159

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
GDAdata collection
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→47.11 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 775 5.06 %Random selection
Rwork0.1959 ---
obs-11673 80.7 %-
Refinement stepCycle: LAST / Resolution: 2.02→47.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 0 1822

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