PDB-9wsg: ToFrO 15E_to_15Z_1ns

ID or keywords:

Entry

Database: PDB / ID: 9wsg

Title

ToFrO 15E_to_15Z_1ns

Components

histidine kinase

Keywords

FLUORESCENT PROTEIN / cyanobacteria / cyanobacteriochrome / pcb / photoreceptor / water molecules

Function / homology

PHYCOCYANOBILIN / :

Function and homology information

Biological species

Tolypothrix sp. PCC 7910 (bacteria)

Method

X-RAY DIFFRACTION /

FREE ELECTRON LASER /

MOLECULAR REPLACEMENT / Resolution: 2.601 Å

Authors

Kim, Y. / Yang, H.W. / Liu, X. / Liu, H. / Park, Y.I. / Yun, J.H.

Funding support

Korea, Republic Of, 2items

Citation

Journal: To Be Published
Title: ToFrO 15E_to_15Z_1ns
Authors: Kim, Y. / Yang, H.W. / Liu, X. / Liu, H. / Park, Y.I. / Yun, J.H.

History

Deposition	Sep 13, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 16, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9wsg.cif.gz	133 KB	Display	PDBx/mmCIF format
PDB format	pdb9wsg.ent.gz	103.7 KB	Display	PDB format
PDBx/mmJSON format	9wsg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ws/9wsg ftp://data.pdbj.org/pub/pdb/validation_reports/ws/9wsg	HTTPS FTP

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Related structure data

Related structure data	9ws1S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: histidine kinase

A: histidine kinase

hetero molecules

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

1

B: histidine kinase

hetero molecules

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

2

A: histidine kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.040, 53.870, 79.950
Angle α, β, γ (deg.)	90.000, 101.150, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	histidine kinase Mass: 20790.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tolypothrix sp. PCC 7910 (bacteria) / Gene: HCG51_32595 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6G9SQI3, histidine kinase
#2: Chemical	ChemComp-CYC / PHYCOCYANOBILIN Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.49 Å³/Da / Density % sol: 50.64 %
Crystal grow	Temperature: 293.15 K / Method: microbatch Details: 5% (w/v) 1-Ethyl-3-methylimidazolium trifluoromethanesulfonate and 15% (w/v) PEG 20,000

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Data collection

Diffraction	Mean temperature: 293.15 K / Serial crystal experiment: N
Diffraction source	Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å
Detector	Type: CS-PAD CXI-2 / Detector: PIXEL / Date: Mar 18, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3 Å / Relative weight: 1
Reflection	Resolution: 2.6→19.82 Å / Num. obs: 12753 / % possible obs: 100 % / Redundancy: 134.19 % / CC_1/2: 0.79 / Net I/σ(I): 4.58
Reflection shell	Resolution: 2.6→2.64 Å / Num. unique obs: 614 / CC_1/2: 0.52

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
Coot		model building
CrystFEL		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 9WS1

9ws1

Resolution: 2.601→18.505 Å / Cor.coef. F_o:F_c: 0.851 / Cor.coef. F_o:F_c free: 0.832 / Cross valid method: FREE R-VALUE / ESU R: 1.028 / ESU R Free: 0.354
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2829	639	5.027 %
R_work	0.2718	12072	-
all	0.272	-	-
obs	-	12711	99.476 %

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: 17.629 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.109 Å²	-0 Å²	-0.01 Å²
2-	-	-0.295 Å²	0 Å²
3-	-	-	0.177 Å²

Refinement step

Cycle: LAST / Resolution: 2.601→18.505 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2435	0	86	167	2688

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	2575
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	2419
X-RAY DIFFRACTION	r_angle_refined_deg	1.703	1.821	3514
X-RAY DIFFRACTION	r_angle_other_deg	2.931	1.799	5505
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.47	5	308
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	1.317	5	12
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.614	10	410
X-RAY DIFFRACTION	r_dihedral_angle_other_3_deg	18.346	10	2
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.486	10	115
X-RAY DIFFRACTION	r_chiral_restr	0.049	0.2	394
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3071
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	581
X-RAY DIFFRACTION	r_nbd_refined	0.19	0.2	486
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.22	0.2	2298
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1253
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.105	0.2	1419
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.254	0.2	57
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.113	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.653	0.2	35
X-RAY DIFFRACTION	r_nbd_other	0.623	0.2	89
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.901	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	1.605	2.042	1244
X-RAY DIFFRACTION	r_mcbond_other	1.599	2.042	1244
X-RAY DIFFRACTION	r_mcangle_it	2.372	3.656	1548
X-RAY DIFFRACTION	r_mcangle_other	2.371	3.659	1549
X-RAY DIFFRACTION	r_scbond_it	1.689	1.959	1331
X-RAY DIFFRACTION	r_scbond_other	1.688	1.958	1330
X-RAY DIFFRACTION	r_scangle_it	2.368	3.605	1966
X-RAY DIFFRACTION	r_scangle_other	2.368	3.604	1966
X-RAY DIFFRACTION	r_lrange_it	2.88	21.568	2880
X-RAY DIFFRACTION	r_lrange_other	2.843	21.394	2858

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
2.601-2.667	0.345	31	0.329	872	0.33	905	0.934	0.928	99.779	0.338
2.667-2.738	0.337	42	0.352	868	0.351	913	0.914	0.917	99.6714	0.361
2.738-2.816	0.407	40	0.336	813	0.339	859	0.87	0.921	99.3015	0.349
2.816-2.9	0.389	41	0.329	808	0.332	850	0.898	0.93	99.8824	0.341
2.9-2.993	0.314	53	0.313	768	0.313	822	0.92	0.935	99.8783	0.341
2.993-3.095	0.355	43	0.321	753	0.323	799	0.923	0.93	99.6245	0.348
3.095-3.209	0.385	36	0.312	728	0.316	766	0.906	0.934	99.7389	0.337
3.209-3.335	0.288	46	0.302	693	0.301	740	0.941	0.937	99.8649	0.351
3.335-3.479	0.274	39	0.282	697	0.282	736	0.94	0.945	100	0.331
3.479-3.642	0.276	36	0.249	631	0.25	667	0.954	0.958	100	0.303
3.642-3.831	0.286	31	0.245	646	0.246	677	0.947	0.96	100	0.297
3.831-4.052	0.303	35	0.225	571	0.229	608	0.928	0.964	99.6711	0.279
4.052-4.317	0.291	24	0.227	541	0.229	566	0.942	0.966	99.8233	0.282
4.317-4.642	0.19	28	0.198	528	0.197	556	0.979	0.974	100	0.25
4.642-5.053	0.216	30	0.224	486	0.224	516	0.968	0.967	100	0.281
5.053-5.598	0.25	21	0.236	445	0.237	467	0.961	0.962	99.7859	0.281
5.598-6.368	0.217	17	0.269	395	0.266	413	0.989	0.95	99.7579	0.3
6.368-7.578	0.193	15	0.256	350	0.254	365	0.979	0.965	100	0.286
7.578-9.917	0.149	17	0.235	286	0.23	303	0.988	0.97	100	0.26
9.917-18.505	0.136	14	0.146	192	0.145	208	0.987	0.989	99.0385	0.185

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