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- PDB-8ovy: Structure of analogue of superfolded GFP -

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Basic information

Entry
Database: PDB / ID: 8ovy
TitleStructure of analogue of superfolded GFP
ComponentsGreen fluorescent protein
KeywordsTRANSLATION
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 / MOLECULAR REPLACEMENT / Resolution: 1.537 Å
AuthorsDunkelmann, D. / Fiedler, M. / Bellini, D. / Alvira, C.P. / Chin, J.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Nature / Year: 2024
Title: Adding alpha , alpha-disubstituted and beta-linked monomers to the genetic code of an organism.
Authors: Dunkelmann, D.L. / Piedrafita, C. / Dickson, A. / Liu, K.C. / Elliott, T.S. / Fiedler, M. / Bellini, D. / Zhou, A. / Cervettini, D. / Chin, J.W.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / struct_ref
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_ref.pdbx_align_begin

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)55,9672
Polymers55,9672
Non-polymers00
Water2,864159
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,9831
Polymers27,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,9831
Polymers27,9831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.516, 37.721, 91.795
Angle α, β, γ (deg.)90.000, 106.376, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-483-

HOH

31B-303-

HOH

41B-373-

HOH

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Components

#1: Protein Green fluorescent protein


Mass: 27983.307 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.93 Å3/Da / Density % sol: 36.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG 3350/PEG 1K/MPD (1:1:1) 37.5%, Bicine/Trizma 0.1 M pH 8.5, Morpheus III Alkaloids 0.8% w/v, Morpheus Alcohols 0.12 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.84 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 1.537→88.071 Å / Num. obs: 59575 / % possible obs: 93.1 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rrim(I) all: 0.11 / Net I/σ(I): 5.1
Reflection shellResolution: 1.537→1.595 Å / Num. unique obs: 5803 / CC1/2: 0.34 / Rrim(I) all: 1.35

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.537→88.071 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.218 / SU B: 1.74 / SU ML: 0.062 / Average fsc free: 0.9124 / Average fsc work: 0.9236 / Cross valid method: FREE R-VALUE / ESU R: 0.09 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2145 2978 4.999 %
Rwork0.1858 56597 -
all0.187 --
obs-59575 92.414 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.863 Å2
Baniso -1Baniso -2Baniso -3
1--0.578 Å20 Å2-0.501 Å2
2--0.539 Å20 Å2
3---0.284 Å2
Refinement stepCycle: LAST / Resolution: 1.537→88.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 477 159 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133704
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173370
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6675002
X-RAY DIFFRACTIONr_angle_other_deg1.4061.5977848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3025444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3423.608194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38215628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1631516
X-RAY DIFFRACTIONr_chiral_restr0.080.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024104
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02752
X-RAY DIFFRACTIONr_nbd_refined0.3420.2529
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.23011
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21668
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2126
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.213
X-RAY DIFFRACTIONr_nbd_other0.20.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2330.27
X-RAY DIFFRACTIONr_mcbond_it1.6721.7771794
X-RAY DIFFRACTIONr_mcbond_other1.6691.7751792
X-RAY DIFFRACTIONr_mcangle_it2.4072.6682232
X-RAY DIFFRACTIONr_mcangle_other2.4072.6682232
X-RAY DIFFRACTIONr_scbond_it3.1282.1431910
X-RAY DIFFRACTIONr_scbond_other3.1272.1431911
X-RAY DIFFRACTIONr_scangle_it4.9193.0562770
X-RAY DIFFRACTIONr_scangle_other4.9193.0572771
X-RAY DIFFRACTIONr_lrange_it5.9320.4723729
X-RAY DIFFRACTIONr_lrange_other5.92320.3933709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.537-1.5770.3132130.28939280.29147680.7770.78186.84980.281
1.577-1.620.3172260.25443120.25745920.8210.85198.8240.245
1.62-1.6670.2492030.2242190.22244590.8830.89599.17020.215
1.667-1.7180.2452070.20340260.20543570.8950.91397.1540.2
1.718-1.7750.2221960.19835150.19942360.9150.92387.60620.195
1.775-1.8370.222230.17838530.1841060.9290.94199.26940.181
1.837-1.9060.1911560.16931740.1739040.9430.95185.29710.172
1.906-1.9840.2011330.17826700.17938350.9420.94673.090.185
1.984-2.0720.2181700.1731240.17236290.9370.95590.76880.18
2.072-2.1730.2241730.18531190.18734870.9340.94794.40780.203
2.173-2.2910.2111500.17328110.17533420.9410.9588.59960.194
2.291-2.430.1981380.17229810.17331440.9470.95399.20480.2
2.43-2.5970.2111380.18228130.18329780.9470.95399.09340.22
2.597-2.8050.2191310.1822990.18227590.9470.95588.07540.221
2.805-3.0720.2411270.19224170.19525680.9360.94499.06540.242
3.072-3.4350.2031210.17321190.17523170.950.95896.67670.226
3.435-3.9650.205740.17615180.17720560.9490.9677.43190.227
3.965-4.8540.147800.15816690.15817520.9680.9799.82880.237
4.854-6.8540.196790.20912850.20813700.9640.9699.5620.332
6.854-88.0710.29400.2257440.2288050.9370.96397.39130.333

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