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- PDB-6yln: mTurquoise2 SG P212121 - Directional optical properties of fluore... -

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Basic information

Entry
Database: PDB / ID: 6yln
TitlemTurquoise2 SG P212121 - Directional optical properties of fluorescent proteins
ComponentsEGFP
KeywordsFLUORESCENT PROTEIN / GFP / mTurquoise2
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / : / EGFP
Function and homology information
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMyskova, J. / Rybakova, O. / 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
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Directional optical properties of fluorescent proteins
Authors: Myskova, J. / 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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)27,7392
Polymers27,7001
Non-polymers391
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint0 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.170, 61.270, 68.640
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: 27700.178 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Gene: EGFP / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1V0D974
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.12 Å3/Da / Density % sol: 42.01 %
Description: A - long axis of crystal B, C - diagonal to the crystal faces
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, HEPES, Magnesium chloride / PH range: 8.0 - 8.5

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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 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.85→39.27 Å / Num. obs: 18997 / % possible obs: 99.9 % / Redundancy: 12.613 % / Biso Wilson estimate: 38.631 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.053 / Χ2: 1.078 / Net I/σ(I): 29.51 / Num. measured all: 239608 / Scaling rejects: 366
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
1.85-1.96.8091.9060.959363138613750.4962.05899.2
1.9-1.957.0881.2611.489498134013400.6661.36100
1.95-2.017.4070.9671.939637130313010.7711.03999.8
2.01-2.077.8840.6922.8310020127112710.8380.741100
2.07-2.148.770.5453.8610928124812460.8980.57899.8
2.14-2.219.9350.5044.6711962120412040.9390.53100
2.21-2.2910.8510.3886.5612479115011500.9670.407100
2.29-2.3911.4830.2978.5812735110911090.9810.311100
2.39-2.4911.7180.22311.8112620107710770.990.234100
2.49-2.6211.8870.16516.0112137102110210.9960.172100
2.62-2.7611.6970.13220.06116629979970.9960.138100
2.76-2.9313.0450.09428.13120939279270.9980.098100
2.93-3.1317.4950.06346.02152738738730.9990.065100
3.13-3.3818.8490.04765.061558882782710.048100
3.38-3.720.3460.03880.221546376076010.039100
3.7-4.1423.7180.031103.81641369269210.032100
4.14-4.7823.650.025125.411471062262210.026100
4.78-5.8523.0280.027122.51220553053010.028100
5.85-8.2723.1920.032109.85990342742710.033100
8.27-39.2719.8350.023128.93491925424810.02497.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ztf

3ztf


Resolution: 1.85→39.27 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.936 / SU ML: 0.111 / SU R Cruickshank DPI: 0.1446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 950 5 %RANDOM
Rwork0.184 ---
obs0.1858 18046 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.51 Å2 / Biso mean: 42.372 Å2 / Biso min: 23.86 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å20 Å2
2--1.09 Å2-0 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.85→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 1 65 1842
Biso mean--71.54 42.16 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191832
X-RAY DIFFRACTIONr_bond_other_d0.0020.021689
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.9632488
X-RAY DIFFRACTIONr_angle_other_deg0.94533886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4365227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92225.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26615293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.449156
X-RAY DIFFRACTIONr_chiral_restr0.1090.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 68 -
Rwork0.346 1299 -
all-1367 -
obs--99.06 %

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