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- PDB-6ylm: mCherry -

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Basic information

Entry
Database: PDB / ID: 6ylm
TitlemCherry
ComponentsmCherry
KeywordsFLUORESCENT PROTEIN / mCherry
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / PAmCherry1 protein
Function and homology information
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1.2Jan 24, 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

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Assembly

Deposited unit
A: mCherry
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5829
Polymers30,2981
Non-polymers2848
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-78 kcal/mol
Surface area10460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.280, 42.920, 85.770
Angle α, β, γ (deg.)90.000, 128.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-13-

ARG

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Components

#1: Protein mCherry


Mass: 30297.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: D1MPT3*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.56 Å3/Da / Density % sol: 51.88 %
Description: A - in crystal plane, perpendicular to long crystal axis B - long crystal axis C - at 129 degrees from the crystal plane
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: PEG 6000, tri-sodium citrate, lithium 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: 1.5419 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.6→67.12 Å / Num. obs: 39100 / % possible obs: 96 % / Redundancy: 6.158 % / Biso Wilson estimate: 29.347 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 1.025 / Net I/σ(I): 14.8 / Num. measured all: 240760 / Scaling rejects: 369
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
1.6-1.644.4181.2231.0910713296324250.5061.38481.8
1.64-1.696.0431.0271.6215585290925790.671.12488.7
1.69-1.746.460.7782.2316673282525810.8090.84591.4
1.74-1.796.5360.5753.0917124278026200.8780.62494.2
1.79-1.856.6530.4573.9917352264826080.9230.49598.5
1.85-1.916.6930.3175.7917167259525650.9620.34398.8
1.91-1.986.6480.2327.6816367247924620.9760.25199.3
1.98-2.076.6310.17210.4916073243724240.9860.18699.5
2.07-2.166.5450.14312.3914902228822770.9910.15699.5
2.16-2.266.520.12614.1614423222222120.9910.13799.5
2.26-2.396.4040.09717.2413384210620900.9950.10699.2
2.39-2.536.2520.08419.4712529201720040.9960.09299.4
2.53-2.75.9580.07321.3810897184718290.9960.0899
2.7-2.925.270.05725.439138174817340.9970.06499.2
2.92-3.24.2550.04927.076732162815820.9970.05697.2
3.2-3.585.0010.03735.667011146914020.9980.04295.4
3.58-4.136.4950.03245.658229129412670.9990.03597.9
4.13-5.066.7270.02749.687312110010870.9990.02998.8
5.06-7.166.8710.02947.84600588487410.03298.9
7.16-67.126.5770.02550.1731444974780.9990.02796.2

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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: 2h5q

2h5q


Resolution: 1.6→67.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.2002 / WRfactor Rwork: 0.1877 / FOM work R set: 0.7311 / SU B: 2.289 / SU ML: 0.081 / SU R Cruickshank DPI: 0.0855 / SU Rfree: 0.0816 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 1173 3 %RANDOM
Rwork0.2009 ---
obs0.2014 37956 96.41 %-
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: 73.59 Å2 / Biso mean: 28.22 Å2 / Biso min: 15.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.01 Å2
2---0.45 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 1.6→67.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1811 0 8 153 1972
Biso mean--36.62 34.46 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191916
X-RAY DIFFRACTIONr_bond_other_d0.0020.021770
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.972592
X-RAY DIFFRACTIONr_angle_other_deg1.42434114
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.0625.062243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.21724.73193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95915339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1671510
X-RAY DIFFRACTIONr_chiral_restr0.0930.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212194
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 72 -
Rwork0.33 2342 -
all-2414 -
obs--81.69 %

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