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- PDB-5y8q: ZsYellow at pH 8.0 -

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Basic information

Entry
Database: PDB / ID: 5y8q
TitleZsYellow at pH 8.0
ComponentsGFP-like fluorescent chromoprotein FP538
KeywordsFLUORESCENT PROTEIN / ZsYellow / pH
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / GFP-like fluorescent chromoprotein FP538
Function and homology information
Biological speciesZoanthus sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsBae, J.E. / Kim, I.J. / Nam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation of KoreaNRF-2017R1D1A1B03033087 Korea, Republic Of
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Disruption of the hydrogen bonding network determines the pH-induced non-fluorescent state of the fluorescent protein ZsYellow by protonation of Glu221.
Authors: Bae, J.E. / Kim, I.J. / Nam, K.H.
History
DepositionAug 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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: GFP-like fluorescent chromoprotein FP538
B: GFP-like fluorescent chromoprotein FP538


Theoretical massNumber of molelcules
Total (without water)52,8332
Polymers52,8332
Non-polymers00
Water1,00956
1
A: GFP-like fluorescent chromoprotein FP538
B: GFP-like fluorescent chromoprotein FP538

A: GFP-like fluorescent chromoprotein FP538
B: GFP-like fluorescent chromoprotein FP538


Theoretical massNumber of molelcules
Total (without water)105,6664
Polymers105,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area9040 Å2
ΔGint-40 kcal/mol
Surface area35600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.410, 72.883, 123.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein GFP-like fluorescent chromoprotein FP538 / zFP538


Mass: 26416.412 Da / Num. of mol.: 2 / Mutation: M129V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9U6Y4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsResidue LYS 66, TYR 67 and GLY 68 are modified to make chromophore (CH7 66). ZsYellow chromophore ...Residue LYS 66, TYR 67 and GLY 68 are modified to make chromophore (CH7 66). ZsYellow chromophore has a three-ring feature by hetero-cyclization of the Lys66 residue, resulting in backbone cleavage between Phe65 and Lys66.

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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 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / Details: Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 9367 / % possible obs: 92 % / Redundancy: 3.1 % / Net I/σ(I): 18.33

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OGR

2ogr


Resolution: 2.9→19.91 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.882 / SU B: 13.707 / SU ML: 0.265 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23613 455 4.9 %RANDOM
Rwork0.17443 ---
obs0.1774 8909 91.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.289 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0 Å2
2---0.74 Å20 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 2.9→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 0 56 3660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193704
X-RAY DIFFRACTIONr_bond_other_d0.0020.023478
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9714986
X-RAY DIFFRACTIONr_angle_other_deg0.78538054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4435441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36324.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89515643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6111512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214125
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7262.7291784
X-RAY DIFFRACTIONr_mcbond_other1.7252.7291783
X-RAY DIFFRACTIONr_mcangle_it2.8784.0852217
X-RAY DIFFRACTIONr_mcangle_other2.8774.0852218
X-RAY DIFFRACTIONr_scbond_it1.8522.9031918
X-RAY DIFFRACTIONr_scbond_other1.8522.9031919
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.134.2682770
X-RAY DIFFRACTIONr_long_range_B_refined5.12121.5064066
X-RAY DIFFRACTIONr_long_range_B_other5.1221.514067
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 42 -
Rwork0.24 622 -
obs--93.79 %

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