PDB-9vf7: Structure of Meiothermus ruber Mrub_1259 LOV domain with N- and C...

ID or keywords:

Entry

Database: PDB / ID: 9vf7

Title

Structure of Meiothermus ruber Mrub_1259 LOV domain with N- and C-terminal alpha helices (MrLOVe)

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: 2.4 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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Download

PDBx/mmCIF format	9vf7.cif.gz	131.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9vf7.ent.gz	95.4 KB	Display	PDB format
PDBx/mmJSON format	9vf7.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/vf/9vf7 ftp://data.pdbj.org/pub/pdb/validation_reports/vf/9vf7	HTTPS FTP

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Related structure data

Related structure data	9vf8C 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

B: histidine kinase

C: histidine kinase

D: histidine kinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	73.294, 77.023, 103.905
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	histidine kinase Mass: 16901.186 Da / Num. of mol.: 4 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.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H₂O
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: 2.12 Å³/Da / Density % sol: 41.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium acetate tetrahydrate 20% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17UM / Wavelength: 0.97919 Å

Detector

Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 22, 2023

Radiation

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

Radiation wavelength

Wavelength: 0.97919 Å / Relative weight: 1

Reflection

Resolution: 2.038→47.281 Å / Num. obs: 24125 / % possible obs: 93.5 % / Redundancy: 7.58 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC_1/2: 0.993 / CC_1/2 anomalous: -0.038 / R_merge(I) obs: 0.2774 / R_pim(I) all: 0.1069 / R_rim(I) all: 0.2977 / AbsDiff over sigma anomalous: 0.783 / B_aniso tensor eigenvalue 1: 14.969 Å² / B_aniso tensor eigenvalue 2: 11.3826 Å² / B_aniso tensor eigenvalue 3: 0 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: 2.839 Å / Aniso diffraction limit 2: 2.273 Å / Aniso diffraction limit 3: 1.969 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): 6.58 / Num. measured all: 182812 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 93 / % possible ellipsoidal: 93.5 / % possible ellipsoidal anomalous: 93 / % possible spherical: 63 / % possible spherical anomalous: 61.4 / Redundancy anomalous: 4.03 / Signal details: averaging_radius = 0.0741/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
6.688-47.281	6.54	0.0631	17.54	7892	7892	1206	1206	0.999	-0.18	0.0266	0.0687	0.637	100	99.8	100	99.8	100	3.81	99.8
5.258-6.688	7.1	0.131	11.96	8568	8568	1206	1206	0.993	-0.045	0.0525	0.1415	0.753	100	99.7	100	99.7	100	3.93	99.7
4.567-5.258	7.34	0.1084	14.83	8848	8848	1206	1206	0.996	-0.128	0.0427	0.1167	0.716	100	99.9	100	99.9	100	3.99	99.9
4.137-4.567	7.48	0.1166	14.67	9025	9025	1206	1206	0.995	-0.148	0.0454	0.1253	0.785	100	99.9	100	99.9	100	4.03	99.9
3.831-4.137	7.56	0.1589	11.86	9120	9120	1207	1207	0.991	-0.049	0.0616	0.1707	0.792	100	100	100	100	100	4.04	100
3.6-3.831	7.61	0.1956	10.09	9175	9175	1206	1206	0.986	-0.085	0.0754	0.21	0.768	100	100	100	100	100	4.05	100
3.416-3.6	7.46	0.2424	8.38	8995	8995	1206	1206	0.982	-0.024	0.0946	0.2606	0.792	100	99.9	100	99.9	100	3.95	99.9
3.26-3.416	7.38	0.321	6.68	8896	8896	1206	1206	0.967	0.024	0.1257	0.3453	0.838	100	99.8	100	99.8	100	3.89	99.8
3.133-3.26	7.45	0.3758	5.66	8990	8990	1207	1207	0.966	0.046	0.1459	0.4038	0.797	100	99.8	100	99.8	100	3.93	99.8
3.021-3.133	7.44	0.4681	4.73	8966	8966	1205	1205	0.936	0.025	0.1821	0.503	0.801	100	100	100	100	100	3.92	100
2.924-3.021	7.52	0.5241	4.13	9079	9079	1207	1207	0.934	-0.034	0.2027	0.5628	0.794	99.9	100	99.9	100	99.9	3.95	100
2.839-2.924	7.13	0.6659	3.37	8595	8595	1206	1206	0.873	0.017	0.2671	0.7187	0.799	99.7	100	99.7	100	99.7	3.73	100
2.757-2.839	7.16	0.7604	2.87	8643	8643	1207	1207	0.866	0.009	0.3038	0.8202	0.802	98	97.9	98	94.6	95.4	3.72	97.9
2.673-2.757	7.54	0.7808	2.92	9090	9090	1205	1205	0.884	-0.021	0.3031	0.8388	0.787	89.1	89.4	89.1	80	80.5	3.92	89.4
2.586-2.673	7.65	0.9574	2.42	9240	9240	1208	1208	0.834	-0.015	0.3673	1.0268	0.803	84.7	85.1	84.7	69.3	69.6	3.98	85.1
2.505-2.586	7.77	1.0758	2.14	9357	9357	1205	1205	0.782	-0.043	0.4097	1.1528	0.772	86.6	87.2	86.6	64.2	64	4.05	87.2
2.423-2.505	7.89	1.1782	1.99	9526	9526	1207	1207	0.729	-0.032	0.4437	1.2608	0.812	85.4	86.2	85.4	56.2	55.6	4.12	86.2
2.334-2.423	8.17	1.2673	1.96	9854	9854	1206	1206	0.734	-0.028	0.467	1.3522	0.794	80.2	81.8	80.2	44.9	43.6	4.31	81.8
2.23-2.334	8.54	1.3076	1.92	10306	10306	1207	1207	0.698	-0.059	0.4701	1.3911	0.786	77.6	79.3	77.6	32.8	31.1	4.53	79.3
2.038-2.23	8.83	1.8989	1.44	10647	10647	1206	1206	0.468	0.029	0.6727	2.0173	0.792	75.9	77.3	75.9	13.5	12.5	4.75	77.3

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AF-D3PRD8-F1

Resolution: 2.4→47.281 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.887 / Matrix type: sparse / SU B: 11.57 / SU ML: 0.261 / Cross valid method: FREE R-VALUE / ESU R: 0.929 / ESU R Free: 0.339
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2794	1031	4.962 %
R_work	0.2299	19747	-
all	0.232	-	-
obs	-	20778	87.901 %

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: 28.683 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.809 Å²	-0 Å²	0 Å²
2-	-	0.141 Å²	-0 Å²
3-	-	-	-0.951 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→47.281 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4271	0	124	49	4444

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.012	4553
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	4281
X-RAY DIFFRACTION	r_angle_refined_deg	1.099	1.811	6255
X-RAY DIFFRACTION	r_angle_other_deg	0.391	1.737	9784
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.197	5	572
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.059	5	41
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.887	10	658
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	11.472	10	195
X-RAY DIFFRACTION	r_chiral_restr	0.047	0.2	720
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5468
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1060
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1013
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.215	0.2	4080
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	2273
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	2186
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	129
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.118	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.793	2.941	2243
X-RAY DIFFRACTION	r_mcbond_other	1.793	2.942	2243
X-RAY DIFFRACTION	r_mcangle_it	2.994	5.273	2803
X-RAY DIFFRACTION	r_mcangle_other	2.994	5.273	2804
X-RAY DIFFRACTION	r_scbond_it	1.886	3.139	2310
X-RAY DIFFRACTION	r_scbond_other	1.884	3.14	2307
X-RAY DIFFRACTION	r_scangle_it	3.128	5.688	3443
X-RAY DIFFRACTION	r_scangle_other	3.128	5.688	3444
X-RAY DIFFRACTION	r_lrange_it	4.986	30.463	5311
X-RAY DIFFRACTION	r_lrange_other	4.986	30.476	5308

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
2.4-2.462	0.359	49	0.268	828	0.272	1700	0.911	0.949	51.5882	0.266
2.462-2.529	0.39	42	0.297	973	0.3	1686	0.866	0.937	60.2017	0.29
2.529-2.603	0.39	50	0.294	1004	0.299	1618	0.886	0.938	65.1422	0.287
2.603-2.682	0.372	47	0.283	1059	0.286	1566	0.927	0.947	70.6258	0.271
2.682-2.77	0.344	52	0.272	1211	0.275	1542	0.901	0.95	81.9066	0.259
2.77-2.867	0.364	79	0.268	1368	0.273	1493	0.912	0.952	96.919	0.254
2.867-2.975	0.312	78	0.253	1355	0.256	1433	0.934	0.955	100	0.241
2.975-3.096	0.291	62	0.256	1333	0.258	1395	0.941	0.954	100	0.239
3.096-3.233	0.323	68	0.241	1264	0.245	1333	0.94	0.963	99.925	0.231
3.233-3.39	0.263	62	0.226	1200	0.228	1264	0.956	0.97	99.8418	0.218
3.39-3.572	0.281	75	0.224	1147	0.227	1222	0.95	0.973	100	0.216
3.572-3.787	0.248	64	0.211	1094	0.213	1158	0.963	0.975	100	0.202
3.787-4.047	0.308	52	0.197	1046	0.201	1098	0.95	0.976	100	0.184
4.047-4.369	0.245	51	0.197	961	0.199	1013	0.97	0.976	99.9013	0.186
4.369-4.782	0.255	51	0.188	897	0.191	948	0.965	0.978	100	0.176
4.782-5.339	0.176	45	0.18	817	0.18	863	0.983	0.981	99.8841	0.168
5.339-6.152	0.27	35	0.234	733	0.235	770	0.953	0.97	99.7403	0.216
6.152-7.503	0.261	27	0.25	635	0.251	662	0.958	0.963	100	0.239
7.503-10.48	0.204	30	0.186	500	0.188	532	0.979	0.98	99.6241	0.185
10.48-47.281	0.202	12	0.304	318	0.301	330	0.961	0.946	100	0.311

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