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- PDB-6l02: Crystal Structure of sfYFP66BPAC203Y -

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Basic information

Entry
Database: PDB / ID: 6l02
TitleCrystal Structure of sfYFP66BPAC203Y
ComponentsYellow fluorescent protein
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Yellow fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsZheng, D. / Yu, L.-J. / Liu, X. / Wang, J.
CitationJournal: CCS Chem / Year: 2021
Title: Ultrafast Photoinduced Electron Transfer in a Photosensitizer Protein
Authors: Zheng, D. / Tao, M. / Yu, L.J. / Liu, X. / Xia, A. / Wang, J.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Yellow fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9981
Polymers26,9981
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10380 Å2
Unit cell
Length a, b, c (Å)51.604, 51.604, 179.053
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 Yellow fluorescent protein


Mass: 26997.514 Da / Num. of mol.: 1
Mutation: S30R,N39I,C48S,V68L,E95C,T105K,E111V,I128T,H148E,K166T,I167V,S205T,A206V,H231L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: yfp / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A059PIR9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsRESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE ...RESIDUE THR 65 HAS BEEN MUTATED TO GLY 65. RESIDUES GLY 65, TYR 66 AND GLY 67 CONSTITUTE THE CHROMOPHORE BF6 66.

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.799→20 Å / Num. obs: 23452 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.02683 / Rpim(I) all: 0.02683 / Rrim(I) all: 0.03795 / Net I/σ(I): 21.84
Reflection shellResolution: 1.799→1.863 Å / Rmerge(I) obs: 0.1802 / Num. unique obs: 2297 / CC1/2: 0.903 / Rpim(I) all: 0.1802 / Rrim(I) all: 0.2548

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YR3

5yr3


Resolution: 1.799→19.518 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 19.09
RfactorNum. reflection% reflection
Rfree0.197 1153 4.92 %
Rwork0.1734 --
obs0.1746 23452 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.94 Å2 / Biso mean: 36.8979 Å2 / Biso min: 19.76 Å2
Refinement stepCycle: final / Resolution: 1.799→19.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 0 139 1949
Biso mean---44.45 -
Num. residues----228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.799-1.88080.26581450.19812726
1.8808-1.97990.25721400.18852727
1.9799-2.10380.24141340.18192718
2.1038-2.2660.23851390.18582768
2.266-2.49360.21581430.17952741
2.4936-2.85350.2321630.18792775
2.8535-3.59140.18391390.17332829
Refinement TLS params.Method: refined / Origin x: -0.2019 Å / Origin y: 7.9467 Å / Origin z: 22.8394 Å
111213212223313233
T0.223 Å20.0039 Å2-0.0054 Å2-0.164 Å20.0117 Å2--0.1976 Å2
L2.0278 °20.1445 °2-0.8058 °2-1.6592 °2-0.3801 °2--2.8501 °2
S0.036 Å °-0.04 Å °-0.0004 Å °0.0295 Å °-0.0327 Å °0.099 Å °-0.0836 Å °-0.3162 Å °-0.0046 Å °
Refinement TLS groupSelection details: all

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