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- PDB-8iz0: mTurquoise2 W66Y -

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Basic information

Entry
Database: PDB / ID: 8iz0
TitlemTurquoise2 W66Y
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: 2.1 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

Downloads & links

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Assembly

Deposited unit
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,7351
Polymers27,7351
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.503, 63.357, 66.428
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: 27735.242 Da / Num. of mol.: 1
Mutation: F64L,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 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.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.95 Å3/Da / Density % sol: 37.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10% 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: 2.1→50 Å / Num. obs: 13253 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.049 / Net I/σ(I): 13.21
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 649 / Rpim(I) all: 0.267 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREP11.6.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→34.27 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.716 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19917 655 5 %RANDOM
Rwork0.17341 ---
obs0.17463 12558 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.158 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3---1.76 Å2
Refinement stepCycle: 1 / Resolution: 2.1→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 0 135 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131877
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171709
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.6642534
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5953991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3095225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82824.3397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96915326
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.798156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
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_it2.5492.839908
X-RAY DIFFRACTIONr_mcbond_other2.5332.834907
X-RAY DIFFRACTIONr_mcangle_it3.5894.2481130
X-RAY DIFFRACTIONr_mcangle_other3.5884.2531131
X-RAY DIFFRACTIONr_scbond_it3.8623.281969
X-RAY DIFFRACTIONr_scbond_other3.8613.285970
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0714.7351405
X-RAY DIFFRACTIONr_long_range_B_refined8.2533.7212021
X-RAY DIFFRACTIONr_long_range_B_other8.20933.5451998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.151 Å
RfactorNum. reflection% reflection
Rfree0.218 51 -
Rwork0.2 881 -
obs--95.88 %

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