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- PDB-6ylq: EGFP in neutral pH, Directionality of Optical Properties of Fluor... -

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Basic information

Entry
Database: PDB / ID: 6ylq
TitleEGFP in neutral pH, Directionality of Optical Properties of Fluorescent Proteins
ComponentseGFP
KeywordsFLUORESCENT PROTEIN / EGFP
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.65 Å
AuthorsMyskova, J. / Rybakova, M. / Brynda, J. / Lazar, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Directionality of light absorption and emission in representative fluorescent proteins.
Authors: Myskova, J. / Rybakova, O. / Brynda, J. / Khoroshyy, P. / Bondar, A. / Lazar, J.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: eGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6863
Polymers28,5691
Non-polymers1162
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-3 kcal/mol
Surface area10360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.940, 62.120, 68.860
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 eGFP


Mass: 28569.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.9 Å3/Da / Density % sol: 35.43 %
Description: A - long axis of crystal B, C - diagonal to the crystal faces
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 8000, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.63→39.39 Å / Num. obs: 24211 / % possible obs: 86.5 % / Redundancy: 5.924 % / Biso Wilson estimate: 26.221 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.084 / Χ2: 0.96 / Net I/σ(I): 15.35 / Num. measured all: 143428 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.63-1.671.7391.6230.55112020366440.2852.07831.6
1.67-1.722.8951.2260.924094199614140.41.44870.8
1.72-1.773.7791.0861.285839193015450.481.23880.1
1.77-1.823.9160.8461.696026189415390.6270.96381.3
1.82-1.884.0910.6052.396137180415000.7770.68783.1
1.88-1.954.2030.4573.316279176514940.8770.51784.6
1.95-2.024.3330.3084.836486169814970.9320.34788.2
2.02-2.14.5250.2546.036891164015230.9530.28692.9
2.1-2.25.9120.2098.28791158814870.9750.22993.6
2.2-2.36.9370.19710.4310267152514800.9810.21397
2.3-2.438.3510.15114.2512000143714370.9910.161100
2.43-2.588.4720.12616.9611632137413730.9940.13499.9
2.58-2.758.3160.10219.8110670128312830.9960.109100
2.75-2.977.9860.08123.359751122112210.9980.087100
2.97-3.267.0850.05131.47857110911090.9990.055100
3.26-3.648.4220.0443.198624102710240.9990.04399.7
3.64-4.218.5080.03351.8176409008980.9990.03599.8
4.21-5.158.1650.02956.3463037747720.9990.03199.7
5.15-7.297.1970.03843.3444556226190.9990.04199.5
7.29-39.397.290.03255.0925663653520.9990.03496.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.65→39.39 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1821 / WRfactor Rwork: 0.151 / FOM work R set: 0.8215 / SU B: 2.742 / SU ML: 0.086 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 1204 5 %RANDOM
Rwork0.1782 ---
obs0.1801 22868 89.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 93.13 Å2 / Biso mean: 24.211 Å2 / Biso min: 14.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.65→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1807 0 474 134 2415
Biso mean--22.62 28.75 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191889
X-RAY DIFFRACTIONr_bond_other_d0.0050.021755
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.9652560
X-RAY DIFFRACTIONr_angle_other_deg0.9834055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9625233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16925.26993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28515316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.351156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212149
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
LS refinement shellResolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 56 -
Rwork0.358 1055 -
all-1111 -
obs--56.89 %

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