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- PDB-8iz1: Single excitation and two emissions pH sensor protein (SITE-pHori... -

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Basic information

Entry
Database: PDB / ID: 8iz1
TitleSingle excitation and two emissions pH sensor protein (SITE-pHorin)_C203E_pH5.0
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: 1.66 Å
AuthorsLi, S.A. / Kang, J.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A unified intracellular pH spectrum with sitepHorin-a quantum-entanglement-based pH-sensitive and ratiometric fluorescent protein
Authors: Kang, J.S. / Li, S.A.
History
DepositionApr 6, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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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)27,7031
Polymers27,7031
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.454, 61.759, 69.655
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: 27703.176 Da / Num. of mol.: 1
Mutation: C48S, F64L, S65T, S72A, N146F, H148G, M153T, V163A, S175G, T203E, 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.: 201 / 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: 2 Å3/Da / Density % sol: 38.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 6000, 100 mm MgCl2, 100 mm Citrate Acid pH 5.0

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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: 1.66→50 Å / Num. obs: 26832 / % possible obs: 99.9 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Net I/σ(I): 34.2
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1346 / Rpim(I) all: 0.242 / % possible all: 99.6

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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: 1.66→34.85 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.327 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 1311 4.9 %RANDOM
Rwork0.17281 ---
obs0.17508 25445 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.66→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 0 203 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131921
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171766
X-RAY DIFFRACTIONr_angle_refined_deg1.8631.6642598
X-RAY DIFFRACTIONr_angle_other_deg1.4241.5964127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3745231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92624100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1615339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.923157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
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_it2.4352.747923
X-RAY DIFFRACTIONr_mcbond_other2.432.743922
X-RAY DIFFRACTIONr_mcangle_it3.5334.1111152
X-RAY DIFFRACTIONr_mcangle_other3.5344.1151153
X-RAY DIFFRACTIONr_scbond_it3.8313.123998
X-RAY DIFFRACTIONr_scbond_other3.8293.126999
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7024.5261445
X-RAY DIFFRACTIONr_long_range_B_refined7.7933.3092087
X-RAY DIFFRACTIONr_long_range_B_other7.6832.6762037
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.662→1.705 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 80 -
Rwork0.297 1823 -
obs--98.7 %

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