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- PDB-6ylo: mTurquoise2 - Directionality of Optical Properties of Fluorescent... -

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Basic information

Entry
Database: PDB / ID: 6ylo
TitlemTurquoise2 - Directionality of Optical Properties of Fluorescent Proteins
ComponentsmTurquoise2_C2221
KeywordsFLUORESCENT PROTEIN / GFP / mTurquoise2
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mTurquoise2_C2221
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1304
Polymers27,7021
Non-polymers4283
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint7 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.820, 90.550, 117.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

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Components

#1: Protein mTurquoise2_C2221


Mass: 27702.150 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.14 Å3/Da / Density % sol: 60.85 %
Description: A - long axis of crystal B - perpendicular to the face of the crystal C - within the crystal plane, perpendicular to the long crystal axis
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3000, Tri-sodium citrate

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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: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.7→58.92 Å / Num. obs: 34680 / % possible obs: 95.9 % / Redundancy: 6.286 % / Biso Wilson estimate: 26.407 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.047 / Net I/σ(I): 17.43 / Num. measured all: 217990 / Scaling rejects: 154
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
1.7-1.741.5660.7770.82489262915890.471.01360.4
1.74-1.792.340.731.125267256522510.5350.90287.8
1.79-1.844.0250.5661.999989252224820.7650.65198.4
1.84-1.94.3510.4942.5710543243124230.8570.56299.7
1.9-1.964.4980.3933.6510598237123560.8710.44699.4
1.96-2.034.8170.274.811032229322900.9420.30399.9
2.03-2.115.0170.2286.2711032220621990.9610.25499.7
2.11-2.195.3420.1827.4111336212821220.980.20299.7
2.19-2.295.0470.218.2410185204320180.970.23598.8
2.29-2.45.4580.1310.7310664195719540.990.14499.8
2.4-2.535.630.11112.8410466186118590.9930.12399.9
2.53-2.696.2980.10215.5111123176717660.9950.11199.9
2.69-2.877.6850.08321.5212950168616850.9970.08999.9
2.87-3.18.1270.06131.1612499154115380.9980.06599.8
3.1-3.49.480.04742.6213765145214520.9990.05100
3.4-3.813.2210.04157.4817240130513040.9990.04399.9
3.8-4.3914.0120.03468.1161141150115010.035100
4.39-5.3814.1570.0371.1142141004100410.031100
5.38-7.613.8990.03561.211091178578510.036100
7.6-58.9212.3020.02472.31557346045310.02598.5

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3ztf


Resolution: 1.7→58.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.567 / SU ML: 0.079 / SU R Cruickshank DPI: 0.0886 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.089 / ESU R Free: 0.089
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2054 1721 5 %RANDOM
Rwork0.1786 ---
obs0.18 32959 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.58 Å2 / Biso mean: 27.059 Å2 / Biso min: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0 Å2-0 Å2
2--1.6 Å20 Å2
3----1.5 Å2
Refinement stepCycle: final / Resolution: 1.7→58.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 22 149 1980
Biso mean--52.14 32.37 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191895
X-RAY DIFFRACTIONr_bond_other_d0.0090.021775
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9762563
X-RAY DIFFRACTIONr_angle_other_deg1.03634101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39325.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.123156
X-RAY DIFFRACTIONr_chiral_restr0.110.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212143
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02432
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 78 -
Rwork0.414 1509 -
all-1587 -
obs--60.43 %

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