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- PDB-8iyy: Single excitation and two emissions pH sensor protein(SITE-pHorin... -

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Basic information

Entry
Database: PDB / ID: 8iyy
TitleSingle excitation and two emissions pH sensor protein(SITE-pHorin)_pH7.0
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / Monomer
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, S.A. / Kang, J.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92054103, 32000855 China
CitationJournal: Sci China Life Sci / Year: 2025
Title: A unified intracellular pH landscape with SITE-pHorin: a quantum-entanglement-enhanced pH probe.
Authors: Li, S.A. / Meng, X.Y. / Zhang, S. / Zhang, Y.J. / Yang, R.Z. / Wang, D.D. / Yang, Y. / Liu, P.P. / Kang, J.S.
History
DepositionApr 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Author supporting evidence / Database references / Category: citation / citation_author / pdbx_audit_support
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_audit_support.grant_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,6771
Polymers27,6771
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.071, 62.092, 70.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Green fluorescent protein


Mass: 27677.205 Da / Num. of mol.: 1
Mutation: C48S, F64L, S65T, S72A, N146F, H148G, M153T, V163A, S175G, T203C, A206K, H231L
Source method: isolated from a genetically manipulated source
Details: Author stated: The SITE-pHorin is the cyan fluorescence protein mTurquoise2 mutant with C48S, S65T, W66Y, D148G, T203C. The mTurquoise2 was firstly designed in the paper (DOI: 10.1038/ncomms1738, PDB ID: 3ztf)
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14% PEG 8000, 100 mm MgCl2, 100 mm HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 10397 / % possible obs: 99.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.106 / Net I/σ(I): 6.57
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.058 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 503 / Rpim(I) all: 0.538 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data collection
HKL-3000data reduction
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.2269 1036 10 %
Rwork0.1775 --
obs-10379 99.8 %
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 484 131 2022
LS refinement shellResolution: 2.3→2.42 Å
RfactorNum. reflection% reflection
Rfree0.28 --
Rwork0.22 --
obs-1286 98 %

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