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- PDB-5y8r: ZsYellow at pH 3.5 -

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Basic information

Entry
Database: PDB / ID: 5y8r
TitleZsYellow at pH 3.5
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: 2.3 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


Theoretical massNumber of molelcules
Total (without water)26,4161
Polymers26,4161
Non-polymers00
Water37821
1
A: GFP-like fluorescent chromoprotein FP538

A: GFP-like fluorescent chromoprotein FP538

A: GFP-like fluorescent chromoprotein FP538

A: 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 operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area9280 Å2
ΔGint-44 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.178, 111.178, 103.751
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

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Components

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


Mass: 26416.412 Da / Num. of mol.: 1 / 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.: 21 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / Details: Na-citrate, NaCl

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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: 2.3→20 Å / Num. obs: 13860 / % possible obs: 94.3 % / Redundancy: 7 % / Net I/σ(I): 39.421

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2ogr


Resolution: 2.3→19.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.564 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.228
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 662 4.8 %RANDOM
Rwork0.2056 ---
obs0.208 13171 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 151.86 Å2 / Biso mean: 68.36 Å2 / Biso min: 35.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å2-0 Å2
2---2.2 Å20 Å2
3---4.4 Å2
Refinement stepCycle: final / Resolution: 2.3→19.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1790 0 0 21 1811
Biso mean---55.49 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191839
X-RAY DIFFRACTIONr_bond_other_d0.0010.021734
X-RAY DIFFRACTIONr_angle_refined_deg1.9811.9722474
X-RAY DIFFRACTIONr_angle_other_deg0.83334012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.095218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59624.4379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56115319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.513156
X-RAY DIFFRACTIONr_chiral_restr0.1120.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212041
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02428
LS refinement shellResolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 49 -
Rwork0.403 919 -
all-968 -
obs--91.23 %

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