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- PDB-5yr3: Structure of sfYFP66BPA -

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Basic information

Entry
Database: PDB / ID: 5yr3
TitleStructure of sfYFP66BPA
ComponentsYellow fluorescent protein
KeywordsFLUORESCENT PROTEIN / Bioluminescence Protein Chromophore Linkage
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Yellow fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsKang, F. / Wang, L. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503704 China
CitationJournal: To Be Published
Title: sfYFP66BPA
Authors: Kang, F. / Wang, L.
History
DepositionNov 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Yellow fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,4351
Polymers25,4351
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10350 Å2
Unit cell
Length a, b, c (Å)51.713, 51.713, 178.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Yellow fluorescent protein


Mass: 25434.551 Da / Num. of mol.: 1
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.: 72 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 15% PEG 3350, 0.1M malic acid, pH 5.0

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29.434 Å / Num. obs: 19926 / % possible obs: 99.2 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 17.7
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.89 / Num. unique obs: 3150 / CC1/2: 0.93 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qyo

1qyo


Resolution: 1.901→29.432 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.72
RfactorNum. reflection% reflection
Rfree0.2896 1993 10 %
Rwork0.2441 --
obs0.2486 19922 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→29.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 0 72 1866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091879
X-RAY DIFFRACTIONf_angle_d1.1352549
X-RAY DIFFRACTIONf_dihedral_angle_d16.3661118
X-RAY DIFFRACTIONf_chiral_restr0.057278
X-RAY DIFFRACTIONf_plane_restr0.005336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.94810.3761380.32851245X-RAY DIFFRACTION100
1.9481-2.00070.33641410.29031263X-RAY DIFFRACTION100
2.0007-2.05960.34981390.30711251X-RAY DIFFRACTION100
2.0596-2.1260.35141400.29251262X-RAY DIFFRACTION100
2.126-2.2020.31941400.30161258X-RAY DIFFRACTION100
2.202-2.29010.35771410.31081272X-RAY DIFFRACTION100
2.2901-2.39430.39081410.30661267X-RAY DIFFRACTION100
2.3943-2.52050.32921440.29041292X-RAY DIFFRACTION100
2.5205-2.67830.33051400.28681268X-RAY DIFFRACTION100
2.6783-2.88490.34511440.29311298X-RAY DIFFRACTION100
2.8849-3.17490.31121450.26741292X-RAY DIFFRACTION100
3.1749-3.63360.29881430.23061291X-RAY DIFFRACTION99
3.6336-4.57520.22441490.18951342X-RAY DIFFRACTION99
4.5752-29.43580.24261480.20631328X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: -0.4003 Å / Origin y: 7.8323 Å / Origin z: 22.8252 Å
111213212223313233
T0.5236 Å20.0319 Å2-0.0019 Å2-0.3154 Å20.0693 Å2--0.4362 Å2
L3.4169 °21.4027 °2-1.5638 °2-4.1404 °2-1.4496 °2--5.3397 °2
S-0.1098 Å °0.0862 Å °0.3812 Å °0.0883 Å °0.2584 Å °0.8882 Å °-0.1526 Å °-0.7802 Å °-0.1406 Å °
Refinement TLS groupSelection details: all

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