PDB-8iz2: Single excitation and two emissions pH sensor protein (SITE-pHori...

ID or keywords:

Entry

Database: PDB / ID: 8iz2

Title

Single excitation and two emissions pH sensor protein (SITE-pHorin)_C203E_pH8.0

Components

Green fluorescent protein

Keywords

FLUORESCENT PROTEIN / monomer

Function / homology

Green 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 species

Aequorea victoria (jellyfish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.572 Å

Authors

Kang, J.S. / Li, S.A.

Funding support

China, 1items

Citation

Journal: 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

Deposition	Apr 6, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Oct 9, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8iz2.cif.gz	70.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8iz2.ent.gz	47.2 KB	Display	PDB format
PDBx/mmJSON format	8iz2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8iz2_validation.pdf.gz	430.5 KB	Display	wwPDB validaton report
Full document	8iz2_full_validation.pdf.gz	430.9 KB	Display
Data in XML	8iz2_validation.xml.gz	15.1 KB	Display
Data in CIF	8iz2_validation.cif.gz	21.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iz/8iz2 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/8iz2	HTTPS FTP

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Related structure data

Related structure data	8iyyC 8iyzC 8iz0C 8iz1C 8iz3C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#174 - Jun 2014 GFP-like Proteins similarity (5) #42 - Jun 2003 Green Fluorescent Protein similarity (5)

Deposited unit

A: Green fluorescent protein

27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	54.024, 62.896, 67.590
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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.: 252 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 40.65 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 8000, MgCl2, Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 5, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.57→50 Å / Num. obs: 32699 / % possible obs: 99.4 % / Redundancy: 12.8 % / R_merge(I) obs: 0.083 / R_pim(I) all: 0.024 / Net I/σ(I): 38
Reflection shell	Resolution: 1.57→1.6 Å / Redundancy: 10.9 % / R_merge(I) obs: 0.35 / Mean I/σ(I) obs: 5.78 / Num. unique obs: 1645 / R_pim(I) all: 0.108 / % possible all: 87.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.572→42.236 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.959 / SU B: 1.331 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1803	1619	4.964 %
R_work	0.1595	30996	-
all	0.161	-	-
obs	-	32615	99.758 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.003 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.009 Å²	-0 Å²	-0 Å²
2-	-	-0.002 Å²	0 Å²
3-	-	-	0.011 Å²

Refinement step

Cycle: LAST / Resolution: 1.572→42.236 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1818	0	22	252	2092

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.013	1919
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	1791
X-RAY DIFFRACTION	r_angle_refined_deg	1.797	1.664	2595
X-RAY DIFFRACTION	r_angle_other_deg	1.574	1.6	4149
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.075	5	234
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.493	24.388	98
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.1	15	333
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.39	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	244
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	2179
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	425
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	287
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	1662
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	899
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.096	0.2	981
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	161
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.271	0.2	8
X-RAY DIFFRACTION	r_nbd_other	0.312	0.2	35
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.165	0.2	14
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.117	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.653	1.611	935
X-RAY DIFFRACTION	r_mcbond_other	1.649	1.606	933
X-RAY DIFFRACTION	r_mcangle_it	2.376	2.418	1169
X-RAY DIFFRACTION	r_mcangle_other	2.377	2.417	1169
X-RAY DIFFRACTION	r_scbond_it	3.274	1.934	984
X-RAY DIFFRACTION	r_scbond_other	3.273	1.935	985
X-RAY DIFFRACTION	r_scangle_it	5.018	2.757	1426
X-RAY DIFFRACTION	r_scangle_other	5.016	2.759	1427
X-RAY DIFFRACTION	r_lrange_it	6.046	20.211	2070
X-RAY DIFFRACTION	r_lrange_other	5.92	19.497	2010

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.572-1.613	0.211	112	0.177	2221	X-RAY DIFFRACTION	98.1489
1.613-1.657	0.201	118	0.172	2192	X-RAY DIFFRACTION	99.8703
1.657-1.705	0.212	128	0.163	2126	X-RAY DIFFRACTION	99.9557
1.705-1.758	0.237	98	0.161	2096	X-RAY DIFFRACTION	100
1.758-1.815	0.208	94	0.149	2028	X-RAY DIFFRACTION	99.9529
1.815-1.879	0.176	108	0.142	1963	X-RAY DIFFRACTION	99.9517
1.879-1.95	0.185	86	0.186	1871	X-RAY DIFFRACTION	99.0385
1.95-2.029	0.177	93	0.148	1837	X-RAY DIFFRACTION	100
2.029-2.119	0.194	97	0.164	1755	X-RAY DIFFRACTION	99.8921
2.119-2.222	0.174	99	0.147	1656	X-RAY DIFFRACTION	100
2.222-2.342	0.211	113	0.175	1578	X-RAY DIFFRACTION	99.8819
2.342-2.484	0.138	68	0.141	1537	X-RAY DIFFRACTION	100
2.484-2.655	0.162	72	0.148	1419	X-RAY DIFFRACTION	100
2.655-2.867	0.167	73	0.153	1352	X-RAY DIFFRACTION	100
2.867-3.139	0.189	72	0.152	1229	X-RAY DIFFRACTION	100
3.139-3.508	0.137	48	0.164	1142	X-RAY DIFFRACTION	100
3.508-4.047	0.171	44	0.147	1013	X-RAY DIFFRACTION	99.9055
4.047-4.946	0.168	45	0.146	868	X-RAY DIFFRACTION	100
4.946-6.955	0.191	27	0.202	696	X-RAY DIFFRACTION	100
6.955-42.236	0.222	24	0.211	417	X-RAY DIFFRACTION	99.7738

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