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- PDB-8iyz: mTurquoise2 S65T -

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Basic information

Entry
Database: PDB / ID: 8iyz
TitlemTurquoise2 S65T
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: 1.99 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)27,7721
Polymers27,7721
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.224, 62.271, 70.502
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: 27772.305 Da / Num. of mol.: 1
Mutation: F64L, S65T, Y66W, S72A, N146F, H148D, M153T, V163A, S175G, 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.: 185 / 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: 2.17 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG 8000, 100 mM MgCl2, 100 mM HEPES PH 6.5

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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: 1.99→50 Å / Num. obs: 15931 / % possible obs: 99.9 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.23 / Rpim(I) all: 0.071 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 6 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 510 / Rpim(I) all: 0.29 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.18.1_3865: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→35.25 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 1582 9.98 %
Rwork0.1612 --
obs0.1671 15851 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→35.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1804 0 0 185 1989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131873
X-RAY DIFFRACTIONf_angle_d1.4512535
X-RAY DIFFRACTIONf_dihedral_angle_d15.224707
X-RAY DIFFRACTIONf_chiral_restr0.084276
X-RAY DIFFRACTIONf_plane_restr0.008331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.060.24191340.19661207X-RAY DIFFRACTION95
2.06-2.130.26291430.19221287X-RAY DIFFRACTION100
2.13-2.220.24891420.17441281X-RAY DIFFRACTION100
2.22-2.320.24981430.17961287X-RAY DIFFRACTION100
2.32-2.440.20211440.1611294X-RAY DIFFRACTION100
2.44-2.590.20041430.15791283X-RAY DIFFRACTION100
2.59-2.790.21921440.16051293X-RAY DIFFRACTION100
2.79-3.070.22381450.1591308X-RAY DIFFRACTION100
3.07-3.520.21460.14451314X-RAY DIFFRACTION100
3.52-4.430.20271490.13781335X-RAY DIFFRACTION100
4.43-35.250.2371490.17371380X-RAY DIFFRACTION98

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