PDB-9o8v: Apo Form of Photoactive Yellow Protein

ID or keywords:

Entry

Database: PDB / ID: 9o8v

Title

Apo Form of Photoactive Yellow Protein

Components

Photoactive yellow protein

Keywords

SIGNALING PROTEIN / Photoreceptor / p-coumaric acid / chromophore / phototaxis

Function / homology

Function and homology information

photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function

Biological species

Halorhodospira halophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.29 Å

Authors

Fried, S.D.E. / Mukherjee, S.M. / Mathews, I.I. / Boxer, S.G.

Funding support

United States, 1items

Citation

Journal: Biorxiv / Year: 2025
Title: Covalent Drug Binding in Live Cells Monitored by Mid-IR Quantum Cascade Laser Spectroscopy: Photoactive Yellow Protein as a Model System.
Authors: Mukherjee, S. / Fried, S.D.E. / Hong, N.Y. / Bagheri, N. / Kozuch, J. / Mathews, I.I. / Kirsh, J.M. / Boxer, S.G.

History

Deposition	Apr 16, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 17, 2025	Group: Database references / Category: citation / citation_author 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9o8v.cif.gz	110.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9o8v.ent.gz	83.9 KB	Display	PDB format
PDBx/mmJSON format	9o8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9o8v_validation.pdf.gz	430.2 KB	Display	wwPDB validaton report
Full document	9o8v_full_validation.pdf.gz	430.5 KB	Display
Data in XML	9o8v_validation.xml.gz	13.9 KB	Display
Data in CIF	9o8v_validation.cif.gz	18.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o8/9o8v ftp://data.pdbj.org/pub/pdb/validation_reports/o8/9o8v	HTTPS FTP

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Related structure data

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	#207 - Mar 2017 Photoactive Yellow Protein similarity (4) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #122 - Feb 2010 Enhanceosome similarity (2) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (2) #183 - Mar 2015 Phototropin similarity (2) #190 - Oct 2015 Two-component Systems similarity (2)

Deposited unit

A: Photoactive yellow protein

B: Photoactive yellow protein

hetero molecules

28 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	104.631, 50.723, 71.252
Angle α, β, γ (deg.)	90.00, 132.93, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Photoactive yellow protein / PYP Mass: 13888.575 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Production host: Escherichia coli (E. coli) / Strain (production host): DH10B / References: UniProt: P16113
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.64 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium Sulfate, Sodium chloride, Potassium phosphate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL12-2 / Wavelength: 0.9795 Å

Detector

Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 6, 2025

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 1.29→40 Å / Num. obs: 66798 / % possible obs: 98.5 % / Redundancy: 4.7 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.065 / R_pim(I) all: 0.033 / R_rim(I) all: 0.073 / Χ²: 2.426 / Net I/σ(I): 13

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.3-1.32	4	0.708	3224	0.729	0.918	0.389	0.811	0.7	95.2
1.32-1.35	4.2	0.617	3271	0.813	0.947	0.33	0.702	0.753	97.5
1.35-1.37	4.4	0.593	3340	0.809	0.946	0.312	0.673	0.787	99.3
1.37-1.4	4.6	0.527	3333	0.852	0.959	0.273	0.596	0.89	98.8
1.4-1.43	4.6	0.464	3292	0.893	0.971	0.239	0.524	0.966	97.9
1.43-1.46	4.4	0.379	3241	0.908	0.976	0.2	0.431	1.091	95.3
1.46-1.5	5	0.325	3366	0.942	0.985	0.163	0.365	1.343	99.8
1.5-1.54	5.1	0.283	3392	0.96	0.99	0.141	0.317	1.55	99.8
1.54-1.59	5.1	0.234	3336	0.972	0.993	0.117	0.262	1.743	99.6
1.59-1.64	5	0.195	3381	0.978	0.994	0.099	0.22	1.973	99.5
1.64-1.7	4.9	0.163	3353	0.98	0.995	0.083	0.183	2.226	99.6
1.7-1.76	4.8	0.14	3379	0.98	0.995	0.073	0.158	2.615	99.6
1.76-1.84	4.7	0.113	3329	0.986	0.997	0.06	0.128	2.953	99.2
1.84-1.94	4.4	0.096	3338	0.987	0.997	0.053	0.11	3.46	97.1
1.94-2.06	4.3	0.081	3245	0.99	0.998	0.044	0.093	3.828	96.6
2.06-2.22	4.8	0.075	3387	0.991	0.998	0.04	0.085	4.17	99.6
2.22-2.45	4.7	0.069	3412	0.993	0.998	0.036	0.078	4.466	99.6
2.45-2.8	4.7	0.063	3388	0.994	0.998	0.033	0.071	4.338	99.1
2.8-3.53	4.4	0.054	3340	0.996	0.999	0.028	0.061	4.291	97.7
3.53-40	4.8	0.048	3451	0.996	0.999	0.024	0.054	3.882	98.5

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Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.29→38.3 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1853	3445	5.16 %
R_work	0.158	-	-
obs	0.1594	66760	98.05 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.29→38.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1752	0	6	171	1929

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	1811
X-RAY DIFFRACTION	f_angle_d	1.352	2451
X-RAY DIFFRACTION	f_dihedral_angle_d	15.881	633
X-RAY DIFFRACTION	f_chiral_restr	0.1	261
X-RAY DIFFRACTION	f_plane_restr	0.01	324

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 (%)
1.29-1.31	0.3132	112	0.2697	2138	X-RAY DIFFRACTION	86
1.31-1.33	0.2771	172	0.2337	2462	X-RAY DIFFRACTION	97
1.33-1.35	0.2488	141	0.2196	2593	X-RAY DIFFRACTION	98
1.35-1.37	0.2342	144	0.2139	2527	X-RAY DIFFRACTION	99
1.37-1.39	0.3138	133	0.2436	2522	X-RAY DIFFRACTION	99
1.39-1.42	0.2737	155	0.2487	2548	X-RAY DIFFRACTION	98
1.42-1.44	0.2434	137	0.223	2446	X-RAY DIFFRACTION	96
1.44-1.47	0.2119	139	0.1886	2467	X-RAY DIFFRACTION	96
1.47-1.5	0.1721	150	0.1419	2534	X-RAY DIFFRACTION	100
1.5-1.53	0.1718	137	0.1344	2618	X-RAY DIFFRACTION	100
1.53-1.57	0.1719	137	0.1337	2549	X-RAY DIFFRACTION	100
1.57-1.61	0.1848	132	0.1352	2566	X-RAY DIFFRACTION	99
1.61-1.65	0.1744	143	0.1466	2564	X-RAY DIFFRACTION	100
1.65-1.7	0.1757	123	0.1514	2557	X-RAY DIFFRACTION	99
1.7-1.76	0.1771	152	0.1421	2579	X-RAY DIFFRACTION	100
1.76-1.82	0.1826	157	0.1363	2556	X-RAY DIFFRACTION	99
1.82-1.89	0.1685	115	0.1369	2533	X-RAY DIFFRACTION	98
1.89-1.98	0.1873	123	0.1343	2456	X-RAY DIFFRACTION	95
1.98-2.08	0.1708	106	0.1453	2592	X-RAY DIFFRACTION	99
2.08-2.21	0.1674	123	0.138	2593	X-RAY DIFFRACTION	100
2.21-2.38	0.1939	133	0.1467	2572	X-RAY DIFFRACTION	100
2.38-2.62	0.1517	145	0.1617	2597	X-RAY DIFFRACTION	99
2.62-3	0.162	132	0.1767	2555	X-RAY DIFFRACTION	98
3-3.78	0.1723	143	0.1618	2538	X-RAY DIFFRACTION	97
3.78-38.3	0.2095	161	0.1567	2653	X-RAY DIFFRACTION	99

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