PDB-8rvx: Cph1 phytochrome PAS-GAF-PHY Y176H mutant

ID or keywords:

Entry

Database: PDB / ID: 8rvx

Title

Cph1 phytochrome PAS-GAF-PHY Y176H mutant

Components

Phytochrome-like protein Cph1

Keywords

FLUORESCENT PROTEIN / Phytochrome / Fluorescent / Phycocyanobilin / PAS / GAF / PHY

Function / homology

Function and homology information

red or far-red light photoreceptor activity / response to red or far red light / red, far-red light phototransduction / protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay sensor kinase activity / protein autophosphorylation / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function

Biological species

Synechocystis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.696 Å

Authors

Nagano, S. / Hughes, J.

Funding support

Germany, 1items

Citation

Journal: Biochemistry / Year: 2025
Title: Integrated Study of Fluorescence Enhancement in the Y176H Variant of Cyanobacterial Phytochrome Cph1.
Authors: Nagano, S. / Song, C. / Rohr, V. / Mackintosh, M.J. / Hoang, O.T. / Kraskov, A. / Yang, Y. / Hughes, J. / Heyne, K. / Mroginski, M.A. / Schapiro, I. / Hildebrandt, P.

History

Deposition	Feb 2, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2025	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8rvx.cif.gz	1005.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8rvx.ent.gz	650.2 KB	Display	PDB format
PDBx/mmJSON format	8rvx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8rvx_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8rvx_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8rvx_validation.xml.gz	81.5 KB	Display
Data in CIF	8rvx_validation.cif.gz	101.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rv/8rvx ftp://data.pdbj.org/pub/pdb/validation_reports/rv/8rvx	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	#183 - Mar 2015 Phototropin similarity (19) #190 - Oct 2015 Two-component Systems similarity (7) #152 - Aug 2012 cAMP-dependent Protein Kinase similarity (4)

Deposited unit

A: Phytochrome-like protein Cph1

B: Phytochrome-like protein Cph1

C: Phytochrome-like protein Cph1

D: Phytochrome-like protein Cph1

hetero molecules

237 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phytochrome-like protein Cph1

B: Phytochrome-like protein Cph1

hetero molecules

defined by author
Evidence: gel filtration, Cph1d2 wild type is known to dimerize upon Pfr formation. doi:10.1016/j.jmb.2011.08.023 Since this Y176H mutant mimics the Pfr conformation, perhaps the assembly found in ...Evidence: gel filtration, Cph1d2 wild type is known to dimerize upon Pfr formation. doi:10.1016/j.jmb.2011.08.023 Since this Y176H mutant mimics the Pfr conformation, perhaps the assembly found in this crystal structure resembles what happens to the protein in solution in context of this truncatd constrct.
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Phytochrome-like protein Cph1

D: Phytochrome-like protein Cph1

hetero molecules

defined by author
Evidence: gel filtration, Cph1d2 wild type is known to dimerize upon Pfr formation. doi:10.1016/j.jmb.2011.08.023 Since this Y176H mutant mimics the Pfr conformation, perhaps the assembly found in ...Evidence: gel filtration, Cph1d2 wild type is known to dimerize upon Pfr formation. doi:10.1016/j.jmb.2011.08.023 Since this Y176H mutant mimics the Pfr conformation, perhaps the assembly found in this crystal structure resembles what happens to the protein in solution in context of this truncatd constrct.
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	135.873, 135.873, 355.644
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	ALA	ALA	19 - 513	19 - 513
2	1	1	ALA	ALA	19 - 513	19 - 513
3	2	2	HIS	HIS	21 - 513	21 - 513
4	2	2	HIS	HIS	21 - 513	21 - 513
5	3	3	ALA	ALA	19 - 513	19 - 513
6	3	3	ALA	ALA	19 - 513	19 - 513
7	4	4	HIS	HIS	21 - 513	21 - 513
8	4	4	HIS	HIS	21 - 513	21 - 513
9	5	5	ALA	ALA	19 - 513	19 - 513
10	5	5	ALA	ALA	19 - 513	19 - 513
11	6	6	HIS	HIS	21 - 513	21 - 513
12	6	6	HIS	HIS	21 - 513	21 - 513

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein	Phytochrome-like protein Cph1 / Bacteriophytochrome Cph1 / Light-regulated histidine kinase 1 Mass: 58783.551 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis (bacteria) / Gene: cph1, slr0473 / Plasmid: pProLAR / Details (production host): Kanamycin resistance / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Pro) / References: UniProt: Q55168, histidine kinase
#2: Chemical	ChemComp-CYC / PHYCOCYANOBILIN Mass: 588.694 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.49 Å³/Da / Density % sol: 64.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.3 M ammonium formate 0.1 M HEPES pH 6.9 18% (w/v) Sokalan CP7

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 3.696→47.651 Å / Num. obs: 36339 / % possible obs: 99.3 % / Redundancy: 25.8 % / CC_1/2: 0.982 / R_merge(I) obs: 0.8 / R_pim(I) all: 0.157 / Net I/σ(I): 6.3
Reflection shell	Resolution: 3.696→3.791 Å / Redundancy: 24.8 % / R_merge(I) obs: 3.702 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4242 / CC_1/2: 0.398 / R_pim(I) all: 0.743 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XDS		data reduction
Aimless		data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.696→47.651 Å / Cor.coef. F_o:F_c: 0.88 / Cor.coef. F_o:F_c free: 0.834 / WR_factor R_free: 0.263 / WR_factor R_work: 0.228 / SU B: 113.504 / SU ML: 0.689 / Average fsc free: 0.9298 / Average fsc work: 0.9453 / Cross valid method: FREE R-VALUE / ESU R Free: 0.779
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3068	1760	4.848 %
R_work	0.2657	34543	-
all	0.268	-	-
obs	-	36303	99.078 %

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: 114.078 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.487 Å²	-0 Å²	0 Å²
2-	-	-0.487 Å²	0 Å²
3-	-	-	0.975 Å²

Refinement step

Cycle: LAST / Resolution: 3.696→47.651 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15506	0	172	4	15682

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	16061
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.016	15146
X-RAY DIFFRACTION	r_ext_dist_refined_b	0.005	0.005	8
X-RAY DIFFRACTION	r_angle_refined_deg	1.338	1.658	21878
X-RAY DIFFRACTION	r_angle_other_deg	0.844	1.587	34766
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.37	5	1942
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.899	5	115
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.402	10	2615
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.312	10	776
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	2445
X-RAY DIFFRACTION	r_chiral_restr_other	1.222	0.2	48
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	18941
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3759
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	4200
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.224	0.2	16114
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.2	8009
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	8553
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	366
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.109	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.368	0.2	49
X-RAY DIFFRACTION	r_nbd_other	0.32	0.2	137
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.443	0.2	11
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.123	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.881	0.842	7789
X-RAY DIFFRACTION	r_mcbond_other	1.881	0.842	7789
X-RAY DIFFRACTION	r_mcangle_it	3.354	1.503	9724
X-RAY DIFFRACTION	r_mcangle_other	3.354	1.504	9725
X-RAY DIFFRACTION	r_scbond_it	1.204	0.839	8272
X-RAY DIFFRACTION	r_scbond_other	1.204	0.839	8273
X-RAY DIFFRACTION	r_scangle_it	2.354	1.533	12154
X-RAY DIFFRACTION	r_scangle_other	2.354	1.533	12155
X-RAY DIFFRACTION	r_lrange_it	6.601	9.036	67632
X-RAY DIFFRACTION	r_lrange_other	6.601	9.036	67633
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.18	0.05	14175
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.164	0.05	14647
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.179	0.05	14340
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.174	0.05	14128
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.186	0.05	14267
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.174	0.05	14367

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.18009	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.18009	0.05007
2	3	A	X-RAY DIFFRACTION	Local ncs	0.16375	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.16375	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.17935	0.05007
3	6	A	X-RAY DIFFRACTION	Local ncs	0.17935	0.05007
4	7	A	X-RAY DIFFRACTION	Local ncs	0.17372	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.17372	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.1863	0.05007
5	10	A	X-RAY DIFFRACTION	Local ncs	0.1863	0.05007
6	11	A	X-RAY DIFFRACTION	Local ncs	0.17405	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.17405	0.05008

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
3.696-3.791	0.366	126	0.364	2372	0.364	2635	0.898	0.903	94.8008	0.356
3.791-3.895	0.329	135	0.336	2440	0.336	2584	0.916	0.911	99.6517	0.328
3.895-4.007	0.391	120	0.327	2361	0.33	2513	0.88	0.919	98.7266	0.309
4.007-4.129	0.322	115	0.294	2296	0.295	2417	0.925	0.942	99.7518	0.277
4.129-4.264	0.355	122	0.283	2233	0.286	2362	0.916	0.944	99.7036	0.259
4.264-4.412	0.339	101	0.265	2186	0.268	2293	0.931	0.95	99.7383	0.237
4.412-4.577	0.285	122	0.26	2091	0.262	2225	0.945	0.954	99.4607	0.229
4.577-4.762	0.299	92	0.235	2035	0.238	2133	0.935	0.962	99.7187	0.206
4.762-4.972	0.289	107	0.237	1939	0.24	2050	0.946	0.961	99.8049	0.202
4.972-5.211	0.331	100	0.266	1868	0.269	1986	0.945	0.956	99.0937	0.217
5.211-5.49	0.287	86	0.263	1761	0.264	1878	0.946	0.955	98.3493	0.223
5.49-5.818	0.336	75	0.283	1721	0.285	1797	0.929	0.945	99.9444	0.242
5.818-6.213	0.3	77	0.28	1615	0.281	1693	0.938	0.95	99.9409	0.233
6.213-6.701	0.333	82	0.277	1495	0.28	1578	0.926	0.947	99.9366	0.239
6.701-7.326	0.332	70	0.26	1392	0.263	1463	0.935	0.954	99.9316	0.221
7.326-8.167	0.252	60	0.213	1265	0.215	1351	0.963	0.969	98.0755	0.18
8.167-9.385	0.218	70	0.186	1128	0.188	1199	0.97	0.978	99.9166	0.167
9.385-11.384	0.214	39	0.194	1013	0.195	1054	0.969	0.979	99.8102	0.186
11.384-15.659	0.253	39	0.222	798	0.223	840	0.967	0.975	99.6429	0.214
15.659-47.651	0.438	22	0.393	534	0.394	561	0.871	0.91	99.1087	0.372

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.4349	0.8925	1.8506	1.6693	0.6813	3.8989	-0.0163	-0.1679	0.1977	0.1912	-0.0178	-0.0803	-0.1564	0.1065	0.0342	1.0706	0.0599	0.0822	1.0336	0.0415	1.1034	3.9257	90.0666	-63.7801
2	1.8393	0.462	0.5278	1.1304	0.5697	0.895	0.0749	-0.1036	-0.2346	0.1335	-0.0379	-0.0758	0.2357	-0.0539	-0.0371	1.0797	0.0191	0.0129	1.0557	0.0169	1.0594	4.5912	74.8076	-72.94
3	1.8393	0.462	0.5278	1.1304	0.5697	0.895	0.0749	-0.1036	-0.2346	0.1335	-0.0379	-0.0758	0.2357	-0.0539	-0.0371	1.0797	0.0191	0.0129	1.0557	0.0169	1.0594	4.5912	74.8076	-72.94
4	2.8708	0.6727	0.1291	0.816	0.7016	0.8196	-0.0944	0.0948	-0.3939	-0.1766	0.0699	-0.0882	0.2817	0.0008	0.0245	1.6071	0.0334	-0.0096	1.5949	0.0062	1.523	-3.3197	40.397	-82.1234
5	3.6965	0.0475	-0.6594	3.0795	-0.2096	2.7955	-0.0113	0.4225	-0.1719	-0.4627	0.0194	-0.0454	0.163	0.1229	-0.0081	1.3863	0.0006	-0.002	1.3495	0.0068	1.3701	-21.2108	33.1505	-53.4298
6	0.4704	0.1667	-0.1115	1.3124	-0.33	0.6501	-0.0062	-0.0007	-0.0114	-0.0194	-0.0019	-0.0461	0.0467	0.0241	0.0082	1.0871	0.0214	-0.0043	1.1964	-0.0038	1.1434	-24.9554	71.258	-56.4942
7	0.4704	0.1667	-0.1115	1.3124	-0.33	0.6501	-0.0062	-0.0007	-0.0114	-0.0194	-0.0019	-0.0461	0.0467	0.0241	0.0082	1.0871	0.0214	-0.0043	1.1964	-0.0038	1.1434	-24.9554	71.258	-56.4942
8	4.7072	2.7209	-2.3106	6.1095	-2.3501	3.9882	-0.1374	0.1894	0.2362	-0.2205	0.1498	0.412	0.1042	-0.1487	-0.0125	1.1567	0.1685	-0.0647	1.1946	-0.0362	1.0873	-22.6308	88.7	-51.6873
9	4.6944	0.5503	-0.5157	2.1595	-1.4535	8.0697	0.1245	-0.5097	-0.5185	0.4669	-0.1063	-0.2042	0.5529	0.15	-0.0181	1.4964	0.0277	0.0001	1.5131	-0.0582	1.5637	-29.3751	50.4074	-15.5661
10	1.4586	0.0277	-0.2279	1.0331	-0.1164	1.1428	0.0048	-0.1759	-0.0117	0.1842	-0.0015	0.1677	0.0359	-0.1322	-0.0033	1.2266	0.0049	-0.0229	1.1905	-0.0063	1.1949	-8.3001	53.2432	-28.2181
11	1.4586	0.0277	-0.2279	1.0331	-0.1164	1.1428	0.0048	-0.1759	-0.0117	0.1842	-0.0015	0.1677	0.0359	-0.1322	-0.0033	1.2266	0.0049	-0.0229	1.1905	-0.0063	1.1949	-8.3001	53.2432	-28.2181
12	2.7001	-1.3615	-1.1304	2.4178	-0.6551	1.4247	-0.0413	0.0488	0.2334	0.0513	0.0216	-0.2962	-0.14	0.2489	0.0197	1.3834	-0.0045	0.0216	1.2764	-0.0132	1.2223	24.8771	76.9166	-33.8593
13	3.4806	-0.0144	0.5695	3.686	-0.6542	2.8872	0.0074	0.4452	0.0879	-0.4204	-0.022	-0.4099	-0.1042	0.315	0.0145	1.2796	-0.0141	-0.0078	1.2811	-0.0196	1.2673	37.8251	69.0768	-3.9246
14	1.2334	0.186	-0.1139	1.3912	0.14	1.0965	-0.0175	0.0862	0.0505	-0.1331	-0.0298	0.1416	-0.0797	-0.1478	0.0472	0.9704	0.0123	-0.0023	0.9841	0.0229	0.9872	25.5738	46.7669	-8.531
15	1.2334	0.186	-0.1139	1.3912	0.14	1.0965	-0.0175	0.0862	0.0505	-0.1331	-0.0298	0.1416	-0.0797	-0.1478	0.0472	0.9704	0.0123	-0.0023	0.9841	0.0229	0.9872	25.5738	46.7669	-8.531
16	0.1126	-0.1588	0.2089	0.3756	-0.1952	0.7849	0.0659	-0.1541	-0.2712	0.026	-0.0185	0.3575	0.3889	-0.4672	-0.0474	1.5067	0.0268	0.0171	1.4848	-0.0225	1.5013	-1.3975	29.5131	-10.5198

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	19 - 170
2	X-RAY DIFFRACTION	2	ALL	A	171 - 327
3	X-RAY DIFFRACTION	3	ALL	A	601 - 602
4	X-RAY DIFFRACTION	4	ALL	A	328 - 513

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