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- PDB-8bvg: Bright fluorescent protein BrUSLEE with subnanosecond fluorescenc... -

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Basic information

Entry
Database: PDB / ID: 8bvg
TitleBright fluorescent protein BrUSLEE with subnanosecond fluorescence lifetime
ComponentsBrUSSLEE
KeywordsFLUORESCENT PROTEIN / BrUSSLEE / GFP-like biomarker
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: 2.38 Å
AuthorsPletnev, V. / Pletneva, N.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Other government Russian Federation
CitationJournal: Int J Mol Sci / Year: 2023
Title: Crystal Structure of Bright Fluorescent Protein BrUSLEE with Subnanosecond Fluorescence Lifetime; Electric and Dynamic Properties.
Authors: Goryacheva, E. / Efremov, R. / Krylov, N. / Artemyev, I. / Bogdanov, A. / Mamontova, A. / Pletnev, S. / Pletneva, N. / Pletnev, V.
History
DepositionDec 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BrUSSLEE
B: BrUSSLEE
C: BrUSSLEE
D: BrUSSLEE
E: BrUSSLEE
F: BrUSSLEE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,96010
Polymers160,5916
Non-polymers3684
Water3,945219
1
A: BrUSSLEE
C: BrUSSLEE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8075
Polymers53,5302
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BrUSSLEE
D: BrUSSLEE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6233
Polymers53,5302
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: BrUSSLEE
F: BrUSSLEE


Theoretical massNumber of molelcules
Total (without water)53,5302
Polymers53,5302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.659, 122.709, 167.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
BrUSSLEE


Mass: 26765.217 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Six subunits in the crystal cell / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 6.4% Tacsimate pH 5.0, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→30 Å / Num. obs: 62234 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 0.998 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.495.60.9361070.6650.4241.0250.67199.3
2.49-2.596.30.76561360.80.3270.8330.69599.9
2.59-2.76.80.6361920.8770.2580.6820.726100
2.7-2.8570.43961180.9470.1770.4740.805100
2.85-3.027.10.29962010.970.120.3230.901100
3.02-3.267.20.17861630.9850.0710.1921.01999.9
3.26-3.587.30.11762070.9920.0470.1261.117100
3.58-4.17.20.08762500.9950.0350.0941.213100
4.1-5.167.20.06863050.9960.0270.0731.322100
5.16-306.90.05665550.9980.0230.0611.332100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EGFP

Resolution: 2.38→29.72 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.3919 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1244 2 %RANDOM
Rwork0.2027 ---
obs0.2041 60921 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.29 Å2 / Biso mean: 63.553 Å2 / Biso min: 29.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å2-0 Å2-0 Å2
2---0.59 Å20 Å2
3---1.22 Å2
Refinement stepCycle: final / Resolution: 2.38→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10926 0 24 219 11169
Biso mean--76.49 54.24 -
Num. residues----1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01411198
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710035
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.66715137
X-RAY DIFFRACTIONr_angle_other_deg1.5221.66323537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53551353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86624.316570
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.178151938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6281536
X-RAY DIFFRACTIONr_chiral_restr0.0740.21411
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212489
X-RAY DIFFRACTIONr_gen_planes_other0.0250.022073
LS refinement shellResolution: 2.38→2.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 68 -
Rwork0.306 3519 -
all-3587 -
obs--77.21 %

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