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- PDB-8iz3: Single excitation and two emissions pH sensor protein(SITE-pHorin... -

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Basic information

Entry
Database: PDB / ID: 8iz3
TitleSingle excitation and two emissions pH sensor protein(SITE-pHorin)_pH5.5
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: 2.18 Å
AuthorsKang, J.S. / Li, S.A.
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)50.925, 62.280, 70.477
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,S72A,S65T,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. 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: 39.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-tris pH5.5, 25%(w/v) PEG3350

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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: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→31.14 Å / Num. obs: 12031 / % possible obs: 99.07 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.086 / Net I/σ(I): 10.67
Reflection shellResolution: 2.183→2.261 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.666 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 1076 / Rpim(I) all: 0.591 / % possible all: 91.26

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Processing

Software
NameVersionClassification
PHENIX(1.18.1_3865: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→31.14 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1203 10 %RANDOM
Rwork0.1701 ---
obs0.1777 12029 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 484 131 1941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011885
X-RAY DIFFRACTIONf_angle_d1.3682550
X-RAY DIFFRACTIONf_dihedral_angle_d8.574246
X-RAY DIFFRACTIONf_chiral_restr0.206277
X-RAY DIFFRACTIONf_plane_restr0.006330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.270.27631210.20861093X-RAY DIFFRACTION92
2.27-2.370.27591330.18271190X-RAY DIFFRACTION100
2.37-2.50.26991310.18751190X-RAY DIFFRACTION100
2.5-2.660.29471340.19171192X-RAY DIFFRACTION100
2.66-2.860.27761330.19141210X-RAY DIFFRACTION100
2.86-3.150.24931340.17851201X-RAY DIFFRACTION100
3.15-3.60.25751360.17131214X-RAY DIFFRACTION100
3.6-4.540.22251360.14121231X-RAY DIFFRACTION100
4.54-31.140.20661450.15691305X-RAY DIFFRACTION100

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