PDB-9vf8: Structure of Meiothermus ruber Mrub_1259 LOV domain (MrLOV)

ID or keywords:

Entry

Database: PDB / ID: 9vf8

Title

Structure of Meiothermus ruber Mrub_1259 LOV domain (MrLOV)

Components

histidine kinase

Keywords

FLUORESCENT PROTEIN / LOV / FMN / photoreceptor / flavoprotein

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function

Biological species

Meiothermus ruber DSM 1279 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.352 Å

Authors

Semenov, O. / Nazarenko, V. / Yudenko, A. / Remeeva, A. / Borshchevskiy, V. / Yang, Y. / Gushchin, I.

Funding support

1items

Citation

Journal: To Be Published
Title: Structures of Meiothermus ruber LOV domains
Authors: Semenov, O. / Nazarenko, V. / Yudenko, A. / Remeeva, A. / Borshchevskiy, V. / Yang, Y. / Gushchin, I.

History

Deposition	Jun 10, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9vf8.cif.gz	38.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vf/9vf8 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/9vf8	HTTPS FTP

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Related structure data

Related structure data	9vf7C 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	#183 - Mar 2015 Phototropin similarity (12) #190 - Oct 2015 Two-component Systems similarity (7) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (2) #207 - Mar 2017 Photoactive Yellow Protein similarity (5) #122 - Feb 2010 Enhanceosome similarity (2)

Deposited unit

A: histidine kinase

hetero molecules

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

1

A: histidine kinase

hetero molecules

A: histidine kinase

hetero molecules

defined by author&software
Evidence: gel filtration
26.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.5930, 78.5930, 73.3810
Angle α, β, γ (deg.)	90.0000, 90.0000, 90.0000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	histidine kinase Mass: 12714.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Meiothermus ruber DSM 1279 (bacteria) / Strain: DSM 1279 / Gene: Mrub_1259, K649_05955 / Production host: Escherichia coli (E. coli) / References: UniProt: D3PRD8, histidine kinase
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
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: 4.31 Å³/Da / Density % sol: 71.47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium sulfate 0.1 M Sodium cacodylate 6.5 30 % w/v PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17UM / Wavelength: 0.97918 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 27, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 3.352→44.303 Å / Num. obs: 2991 / % possible obs: 91.1 % / Redundancy: 21.69 % / CC_1/2: 0.987 / CC_1/2 anomalous: 0.075 / R_merge(I) obs: 0.5299 / R_pim(I) all: 0.1174 / R_rim(I) all: 0.5432 / AbsDiff over sigma anomalous: 0.67 / B_aniso tensor eigenvalue 1: 0 Å² / B_aniso tensor eigenvalue 2: 0 Å² / B_aniso tensor eigenvalue 3: 39.6522 Å² / B_aniso tensor eigenvector 1 ortho1: 1 / B_aniso tensor eigenvector 1 ortho2: 0 / B_aniso tensor eigenvector 1 ortho3: 0 / B_aniso tensor eigenvector 2 ortho1: 0 / B_aniso tensor eigenvector 2 ortho2: 1 / B_aniso tensor eigenvector 2 ortho3: 0 / B_aniso tensor eigenvector 3 ortho1: 0 / B_aniso tensor eigenvector 3 ortho2: 0 / B_aniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 3.347 Å / Aniso diffraction limit 2: 3.347 Å / Aniso diffraction limit 3: 3.68 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 5.13 / Num. measured all: 64878 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 89.9 / % possible ellipsoidal: 91.1 / % possible ellipsoidal anomalous: 89.9 / % possible spherical: 83.4 / % possible spherical anomalous: 82 / Redundancy anomalous: 12.53 / Signal details: averaging_radius = 0.0808/Ang. / Signal type: local

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
7.077-44.303	19.06	0.1207	7.67	8118	8118	426	426	0.989	0.059	0.028	0.1242	0.359	99.6	99.8	99.6	99.8	99.6	12.45	99.8
5.539-7.077	20.93	0.2689	6.49	8959	8959	428	428	0.995	0.155	0.0609	0.2759	0.488	100	100	100	100	100	12.26	100
4.807-5.539	20.39	0.4151	7.02	8708	8708	427	427	0.984	-0.001	0.0974	0.4268	0.579	100	100	100	100	100	11.73	100
4.336-4.807	21.55	0.6439	6.52	9202	9202	427	427	0.984	0.184	0.146	0.6608	0.742	100	99.8	100	99.8	100	12.08	99.8
4.016-4.336	22.82	1.0453	4.59	9768	9768	428	428	0.955	0.05	0.2264	1.0703	0.819	100	100	100	100	100	12.75	100
3.767-4.016	24.17	2.335	2.3	10392	10392	430	430	0.878	-0.047	0.4847	2.3864	0.815	99.7	99.8	99.7	99.8	99.7	13.43	99.8
3.352-3.767	22.9	4.1742	1.34	9731	9731	425	425	0.847	-0.184	0.8687	4.2668	0.768	58.1	59.4	58.1	41.9	41.3	12.86	59.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
STARANISO		data scaling
Aimless		data scaling
REFMAC	5.8.0430	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.352→44.303 Å / Cor.coef. F_o:F_c: 0.91 / Cor.coef. F_o:F_c free: 0.871 / SU B: 33.25 / SU ML: 0.503 / Cross valid method: FREE R-VALUE / ESU R Free: 0.54
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2721	134	4.48 %
R_work	0.2422	2857	-
all	0.244	-	-
obs	-	2991	83.292 %

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: 83.668 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.749 Å²	0 Å²	0 Å²
2-	-	-0.749 Å²	0 Å²
3-	-	-	1.499 Å²

Refinement step

Cycle: LAST / Resolution: 3.352→44.303 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	829	0	31	0	860

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.012	883
X-RAY DIFFRACTION	r_bond_other_d	0	0.016	820
X-RAY DIFFRACTION	r_angle_refined_deg	1.057	1.815	1210
X-RAY DIFFRACTION	r_angle_other_deg	0.315	1.749	1875
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.352	5	104
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	1.338	5	10
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.984	10	128
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	6.739	10	43
X-RAY DIFFRACTION	r_chiral_restr	0.037	0.2	131
X-RAY DIFFRACTION	r_gen_planes_refined	0.001	0.02	1070
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	216
X-RAY DIFFRACTION	r_nbd_refined	0.214	0.2	184
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.254	0.2	782
X-RAY DIFFRACTION	r_nbtor_refined	0.185	0.2	444
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	428
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.187	0.2	11
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.04	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.241	0.2	12
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	71
X-RAY DIFFRACTION	r_mcbond_it	13.027	7.924	419
X-RAY DIFFRACTION	r_mcbond_other	13.024	7.924	419
X-RAY DIFFRACTION	r_mcangle_it	19.237	14.295	522
X-RAY DIFFRACTION	r_mcangle_other	19.219	14.301	523
X-RAY DIFFRACTION	r_scbond_it	12.835	8.659	464
X-RAY DIFFRACTION	r_scbond_other	12.815	8.66	461
X-RAY DIFFRACTION	r_scangle_it	19.433	15.444	688
X-RAY DIFFRACTION	r_scangle_other	19.419	15.435	689
X-RAY DIFFRACTION	r_lrange_it	24.524	83.813	1018
X-RAY DIFFRACTION	r_lrange_other	24.513	83.779	1019

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 (%)
3.352-3.439		0	0.643	29	X-RAY DIFFRACTION	11.5538
3.439-3.532	0.593	3	0.533	61	X-RAY DIFFRACTION	25.9109
3.532-3.634	0.665	3	0.486	97	X-RAY DIFFRACTION	41.841
3.634-3.745	0.345	6	0.469	190	X-RAY DIFFRACTION	80.6584
3.745-3.867	0.552	11	0.443	212	X-RAY DIFFRACTION	98.2379
3.867-4.002	0.137	11	0.36	216	X-RAY DIFFRACTION	100
4.002-4.152	0.358	15	0.298	198	X-RAY DIFFRACTION	100
4.152-4.32	0.415	8	0.234	203	X-RAY DIFFRACTION	100
4.32-4.51	0.247	9	0.217	184	X-RAY DIFFRACTION	99.4845
4.51-4.727	0.286	12	0.223	181	X-RAY DIFFRACTION	100
4.727-4.98	0.192	11	0.179	181	X-RAY DIFFRACTION	100
4.98-5.278	0.222	9	0.192	164	X-RAY DIFFRACTION	100
5.278-5.636	0.149	3	0.182	165	X-RAY DIFFRACTION	100
5.636-6.08	0.217	9	0.221	144	X-RAY DIFFRACTION	100
6.08-6.648	0.28	7	0.245	143	X-RAY DIFFRACTION	100
6.648-7.412	0.315	6	0.206	126	X-RAY DIFFRACTION	100
7.412-8.519	0.433	5	0.203	114	X-RAY DIFFRACTION	100
8.519-10.338	0.232	6	0.164	103	X-RAY DIFFRACTION	100
10.338-14.239		0	0.203	86	X-RAY DIFFRACTION	100
14.239-44.303		0	0.421	60	X-RAY DIFFRACTION	96.7742

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