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- PDB-6zqo: EYFP mutant - F165G -

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Basic information

Entry
Database: PDB / ID: 6zqo
TitleEYFP mutant - F165G
ComponentsG protein/GFP fusion protein
KeywordsFLUORESCENT PROTEIN / Alternative routes of post-translation chemistry
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / symbiont entry into host cell / viral envelope / virion attachment to host cell / membrane
Similarity search - Function
Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
G protein/GFP fusion protein
Similarity search - Component
Biological speciesRecombinant vesicular stomatitis Indiana virus rVSV-G/GFP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPletnev, V.Z. / Pletnev, S.V. / Pletneva, N.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research19-04-00107 Russian Federation
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design.
Authors: Pletneva, N.V. / Maksimov, E.G. / Protasova, E.A. / Mamontova, A.V. / Simonyan, T.R. / Ziganshin, R.H. / Lukyanov, K.A. / Muslinkina, L. / Pletnev, S. / Bogdanov, A.M. / Pletnev, V.Z.
History
DepositionJul 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G protein/GFP fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4182
Polymers28,3221
Non-polymers961
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.888, 57.888, 168.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein G protein/GFP fusion protein


Mass: 28321.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Recombinant vesicular stomatitis Indiana virus rVSV-G/GFP
Gene: G, GFP / Production host: Escherichia coli (E. coli) / References: UniProt: B7UCZ6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 5.7 mg/ml in 20mM Tris 8.0 200 mM NaCl mixed with a 1.44M (NH4)2SO4, 60mM Bicine pH 9.0 reservoir solution.

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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 EIGER X 16M / Detector: PIXEL / Date: Sep 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 14573 / % possible obs: 94.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.028 / Rrim(I) all: 0.066 / Χ2: 0.816 / Net I/σ(I): 9.8 / Num. measured all: 83201
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.50.79414570.8810.3620.8761.02898.4
2.28-2.375.90.61114790.9820.2720.6710.53599.1
2.37-2.485.70.35214930.9840.160.3880.52799.1
2.48-2.615.30.22313890.990.1030.2470.59192.4
2.61-2.776.60.16914830.9970.0710.1840.62998.3
2.77-2.996.60.11715040.9970.0490.1270.74399
2.99-3.296.30.07415030.9970.0320.0810.9498.4
3.29-3.765.40.05814750.9980.0270.0641.06595.1
3.76-4.734.40.04213150.9980.0210.0481.03983.4
4.73-305.10.0414750.9980.0190.0441.24985.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFP

1yfp


Resolution: 2.2→29.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.277 / SU ML: 0.306 / SU R Cruickshank DPI: 0.3214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3396 710 4.9 %RANDOM
Rwork0.2543 ---
obs0.2585 13828 94.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 138.06 Å2 / Biso mean: 64.924 Å2 / Biso min: 32.57 Å2
Baniso -1Baniso -2Baniso -3
1-4.27 Å2-0 Å2-0 Å2
2--4.27 Å2-0 Å2
3----8.54 Å2
Refinement stepCycle: final / Resolution: 2.2→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 5 29 1888
Biso mean--88.82 65.78 -
Num. residues----232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171733
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6622597
X-RAY DIFFRACTIONr_angle_other_deg1.1951.5934040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8575231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28824.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1815326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.061156
X-RAY DIFFRACTIONr_chiral_restr0.0560.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022147
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02392
LS refinement shellResolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 50 -
Rwork0.447 1041 -
all-1091 -
obs--98.55 %

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