PDB-4r38: LOV domain from Erythrobacter litoralis EL346 blue-light activate...

ID or keywords:

Entry

Database: PDB / ID: 4r38

Title

LOV domain from Erythrobacter litoralis EL346 blue-light activated histidine kinase

Components

Blue-light-activated histidine kinase 2

Keywords

SIGNALING PROTEIN / riboflavin / light-activated / LOV domain / photoreceptor / sensory transduction / signal transduction

Function / homology

Function and homology information

histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / ATP binding
Similarity search - Function

Biological species

Erythrobacter litoralis HTCC2594 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Rivera-Cancel, G. / Tomchick, D.R. / Gardner, K.H.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Full-length structure of a monomeric histidine kinase reveals basis for sensory regulation.
Authors: Rivera-Cancel, G. / Ko, W.H. / Tomchick, D.R. / Correa, F. / Gardner, K.H.

History

Deposition	Aug 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 31, 2014	Group: Database references
Revision 1.2	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4r38.cif.gz	267.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4r38.ent.gz	221.5 KB	Display	PDB format
PDBx/mmJSON format	4r38.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/r3/4r38 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/4r38	HTTPS FTP

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Related structure data

Related structure data	4r39C 4r3aC 2pr5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3jqx-3 4co7-1 5j7e-4 2mqi-d 4mfh-1 1rxi-d 5c6c-1 1ljl-d 1o4k-d 5yiz-11 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4r39C

4r3aC

2pr5S

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#183 - Mar 2015 Phototropin similarity (7) #190 - Oct 2015 Two-component Systems similarity (4) #207 - Mar 2017 Photoactive Yellow Protein similarity (3)

Deposited unit

A: Blue-light-activated histidine kinase 2

B: Blue-light-activated histidine kinase 2

C: Blue-light-activated histidine kinase 2

D: Blue-light-activated histidine kinase 2

hetero molecules

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

1

A: Blue-light-activated histidine kinase 2

hetero molecules

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

2

B: Blue-light-activated histidine kinase 2

hetero molecules

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

3

C: Blue-light-activated histidine kinase 2

hetero molecules

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

4

D: Blue-light-activated histidine kinase 2

hetero molecules

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

5

A: Blue-light-activated histidine kinase 2

C: Blue-light-activated histidine kinase 2

hetero molecules

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

6

B: Blue-light-activated histidine kinase 2

D: Blue-light-activated histidine kinase 2

hetero molecules

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

Unit cell

Length a, b, c (Å)	41.081, 89.383, 122.404
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

THE INDIVIDUAL LOV DOMAIN BEHAVES AS A DIMER IN SOLUTION, HOWEVER, THE FULL-LENGTH PROTEIN IS A MONOMER.

#1: Protein	Blue-light-activated histidine kinase 2 / EL346-LOV-histidine kinase / EL346-LOV-HK Mass: 15858.587 Da / Num. of mol.: 4 / Fragment: N-terminal LOV domain, UNP residues 1-134 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Erythrobacter litoralis HTCC2594 (bacteria) Strain: HTCC2594 / Gene: ELI_04860 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2NB77, histidine kinase
#2: Chemical	ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 Mass: 376.364 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₀N₄O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H₂O
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: 1.77 Å³/Da / Density % sol: 30.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% PEG 4000, 0.1 M HEPES, 0.1 M magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97901 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2012 / Details: monochromator

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97901 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. all: 58404 / Num. obs: 58404 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / R_merge(I) obs: 0.057 / Χ²: 1.186

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.6-1.63	3	0.624	1921	0.866	1	64.4
1.63-1.66	3.6	0.642	2338	0.883	1	77.4
1.66-1.69	3.9	0.583	2616	0.964	1	87.3
1.69-1.72	4.2	0.5	2752	0.97	1	91
1.72-1.76	4.5	0.462	2909	1.048	1	96.9
1.76-1.8	4.7	0.369	2990	1.048	1	98.5
1.8-1.85	5	0.302	2982	1.116	1	99.7
1.85-1.9	5.2	0.254	3020	1.232	1	99.7
1.9-1.95	5.2	0.239	3024	1.602	1	99.9
1.95-2.02	5.4	0.154	3012	1.196	1	100
2.02-2.09	5.4	0.136	3030	1.511	1	99.8
2.09-2.17	5.5	0.104	3038	1.236	1	100
2.17-2.27	5.4	0.094	3039	1.473	1	99.9
2.27-2.39	5.5	0.074	3046	1.294	1	100
2.39-2.54	5.6	0.064	3057	1.151	1	100
2.54-2.74	5.5	0.056	3069	1.179	1	99.9
2.74-3.01	5.5	0.052	3064	1.141	1	99.9
3.01-3.45	5.3	0.05	3103	1.132	1	99.8
3.45-4.34	5.1	0.043	3122	1.089	1	99.4
4.34-50	5	0.042	3272	0.964	1	98.4

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.2_1309	refinement
PDB_EXTRACT	3.14	data extraction
HKL-3000		data collection
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2PR5

2pr5

Resolution: 1.6→37.117 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 31.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2244	2941	5.1 %	RANDOM
R_work	0.1997	-	-	-
all	0.201	57709	-	-
obs	0.201	57709	95.51 %	-

Solvent computation

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

Displacement parameters

B_iso max: 157.83 Å² / B_iso mean: 52.7748 Å² / B_iso min: 22.8 Å²

Refine analyze

Luzzati sigma a obs: 0.2 Å

Refinement step

Cycle: LAST / Resolution: 1.6→37.117 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3466	0	108	145	3719

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	3650
X-RAY DIFFRACTION	f_angle_d	1.289	4934
X-RAY DIFFRACTION	f_chiral_restr	0.075	508
X-RAY DIFFRACTION	f_plane_restr	0.006	656
X-RAY DIFFRACTION	f_dihedral_angle_d	13.805	1342

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6262	0.3648	108	0.3144	1749	1857	66
1.6262-1.6543	0.3423	113	0.2957	2115	2228	78
1.6543-1.6844	0.326	142	0.2842	2265	2407	86
1.6844-1.7168	0.3261	130	0.2745	2419	2549	89
1.7168-1.7518	0.3409	121	0.2774	2564	2685	95
1.7518-1.7899	0.3079	125	0.2733	2678	2803	97
1.7899-1.8315	0.3289	137	0.2633	2654	2791	99
1.8315-1.8773	0.296	128	0.2496	2722	2850	99
1.8773-1.9281	0.32	145	0.2687	2693	2838	99
1.9281-1.9848	0.2504	164	0.2218	2665	2829	100
1.9848-2.0489	0.2521	145	0.2069	2724	2869	100
2.0489-2.1221	0.2476	144	0.2235	2681	2825	100
2.1221-2.2071	0.2653	145	0.2103	2716	2861	100
2.2071-2.3075	0.2399	136	0.2035	2709	2845	99
2.3075-2.4291	0.2186	158	0.1837	2721	2879	100
2.4291-2.5813	0.2075	151	0.1815	2738	2889	100
2.5813-2.7805	0.2098	154	0.187	2711	2865	100
2.7805-3.0602	0.2417	122	0.197	2775	2897	100
3.0602-3.5028	0.2066	153	0.1893	2776	2929	100
3.5028-4.412	0.1989	155	0.172	2774	2929	99
4.412-37.1271	0.1889	165	0.192	2919	3084	99

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	0.1114	0.0704	-0.0106	0.0655	-0.0542	0.0677	0.1317	0.0587	-0.0953	0.0444	-0.3074	0.3334	0.1772	0.077	-0.0001	0.4826	0.0416	-0.0294	0.3395	-0.0606	0.4008	5.1235	1.0222	33.1594
2	0.1111	0.0518	0.0079	0.0221	0.0074	0.0517	-0.0172	0.0372	0.0955	0.1922	-0.217	0.0798	0.2104	-0.209	0.0002	0.4036	0.0187	0.0015	0.422	-0.1125	0.3913	-3.1441	5.004	29.9969
3	0.0506	0.0534	0.0379	0.025	0.0141	0.0544	-0.0396	0.307	-0.0773	-0.1772	-0.1959	-0.0538	0.2869	-0.2151	-0.0001	0.4723	0.0533	-0.0043	0.4404	-0.0598	0.3743	5.1652	2.4498	19.7542
4	0.0007	-0.0107	-0.0126	0.0097	-0.0014	0.0152	-0.0249	-0.0509	0.2139	-0.0002	-0.0248	-0.3074	0.1346	0.2448	0	0.4533	0.0757	0.0032	0.4538	-0.0443	0.3923	17.9269	2.3824	22.8337
5	0.1696	-0.1168	-0.1768	0.0044	0.0886	0.1459	0.0749	0.0415	0.1743	-0.0995	-0.0424	-0.1688	-0.2155	0.1252	0	0.457	0.0634	-0.0173	0.3871	-0.0269	0.3639	9.0022	9.5179	24.1321
6	0.2896	0.1711	-0.0657	0.1427	0.0553	0.1061	0.1828	-0.2342	0.1812	0.0081	-0.1656	-0.091	-0.0391	0.1044	0	0.4223	0.0506	-0.0537	0.4041	-0.0357	0.3611	11.3633	3.6487	34.7701
7	1.4831	-0.0699	0.165	-0.0022	0.019	0.077	-0.3489	0.1975	0.3616	0.112	-0.0599	0.0236	1.0452	0.0586	-0.0892	0.7382	-0.0081	0.0286	0.4119	-0.0656	0.308	4.2907	-8.754	45.9241
8	0.8402	-0.3115	0.1734	0.6243	-0.124	0.027	-0.0721	-0.2785	0.2813	-0.0889	-0.0945	-0.0192	0.6886	-0.3958	-0.3832	0.8901	-0.4365	0.0765	0.6448	-0.1419	0.3938	-7.0493	-15.1912	50.2049
9	3.106	-0.4679	1.5177	0.2699	-0.441	1.1192	-0.203	-0.0441	0.557	0.4031	-0.4905	0.0941	0.9789	-0.6555	-0.7691	0.7863	-0.1594	0.1466	0.555	-0.147	0.2342	-3.3906	-7.57	52.2452
10	0.1044	0.0541	0.0102	0.095	-0.0716	0.0633	0.0679	0.1685	0.0825	-0.0786	-0.0677	-0.0096	-0.2875	-0.1537	0	0.3005	0.0391	0.0063	0.3259	-0.0188	0.3435	7.7771	19.9895	47.3478
11	0.0572	0.0297	-0.023	0.0348	0.0134	0.0219	-0.0676	-0.0677	-0.0928	0.2831	-0.1581	0.0717	0.1576	0.5032	-0.0001	0.2734	0.0557	0.0029	0.4261	-0.0053	0.3626	19.1908	19.5211	44.4976
12	0.1874	-0.0107	0.0523	0.0748	0.0393	0.0355	-0.0258	0.0498	0.0824	-0.0813	-0.0057	0.1374	-0.1749	0.1092	-0	0.3506	0.0169	-0.0507	0.3399	0.0242	0.341	12.6924	31.3625	41.8069
13	0.0115	0.0066	-0.0072	0.0017	-0.0079	0.0111	-0.3064	-0.0135	0.2624	-0.1041	0.0472	0.0844	-0.3171	-0.0432	0.0002	0.3809	0.0697	-0.1244	0.3932	0.0025	0.4358	0.3637	32.0298	38.2647
14	0.1367	-0.2111	0.1591	0.3461	-0.0889	0.2767	-0.059	0.0191	-0.0412	-0.139	0.0014	0.039	-0.0537	-0.0902	0	0.2989	-0.0215	-0.03	0.4166	0.0201	0.3354	5.4311	23.3937	38.9571
15	0.0177	0.0588	0.0136	0.1009	0.0697	0.0324	0.1201	0.0474	-0.0203	-0.3024	0.0129	0.0889	-0.0393	-0.0282	-0.0002	0.3124	0.0139	0.0354	0.4245	-0.0176	0.3251	9.5536	20.4476	37.1165
16	0.1822	-0.0935	-0.0967	0.0525	-0.0437	0.1392	-0.0493	-0.1444	-0.0647	-0.0225	-0.0913	-0.0767	0.0666	-0.0365	0	0.2501	-0.0503	-0.003	0.3133	-0.0085	0.3283	6.0031	11.963	58.5812
17	0.022	0.0069	-0.0066	0.0066	0.0122	0.0239	0.0245	0.2073	-0.4011	-0.1468	-0.263	0.0315	-0.0482	-0.1402	0.0002	0.2773	0.0097	0.0068	0.3681	-0.0381	0.3319	-6.2747	9.0104	60.5354
18	0.0079	0.0002	-0.0123	0.0008	-0.0012	0.003	0.1237	0.1147	0.182	0.2736	-0.0732	-0.2464	0.1789	-0.0523	0.0002	0.3237	0.0359	0.0268	0.3305	0.004	0.3824	-3.7908	16.6269	62.3729
19	0.0979	0.0112	-0.0161	0.0488	-0.0151	0.0164	0.051	-0.0815	0.038	0.0984	0.0824	0.1264	0.0629	-0.186	-0	0.3024	0.0216	-0.0044	0.3507	0.0086	0.3581	3.2889	10.9534	71.6529
20	0.01	-0.0075	0.0052	0.0161	-0.0146	0.0265	-0.075	-0.2691	-0.3239	0.3091	-0.0981	-0.2762	0.1415	0.2447	0.0001	0.3667	0.0532	0.008	0.409	0.0467	0.3823	14.5962	4.4819	70.9458
21	0.026	-0.0759	0.0223	0.1263	-0.1697	0.2431	0.0303	-0.0386	-0.0698	0.0715	-0.0309	-0.055	0.1816	0.0328	-0	0.3276	0.0228	0.0261	0.2757	0.0379	0.3695	3.7654	3.6824	68.6701
22	0.0172	-0.0532	-0.0089	0.0284	-0.0192	0.0202	0.108	-0.0148	0.1084	0.1294	-0.0144	-0.0938	0.0891	-0.0764	-0.0001	0.3986	-0.0168	0.0281	0.3189	0.0214	0.3847	3.4217	1.2746	65.932
23	0.0112	-0.0032	0.0175	-0.0003	-0.0151	0.0142	-0.2496	0.0909	-0.1812	0.0326	0.0072	-0.2027	0.1554	0.3103	-0.0002	0.3388	0.084	0.0492	0.3549	0.0303	0.4528	18.7048	8.9996	52.6271
24	0.0295	0.0046	-0.0322	0.0363	0.0244	0.0296	0.0965	-0.0486	-0.1533	-0.1024	-0.1848	-0.0749	0.2837	-0.1412	-0.0001	0.2778	-0.0155	-0.0277	0.3737	0.0331	0.414	2.5112	3.0824	62.4668

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 31 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 50 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 51 through 64 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 65 through 76 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 77 through 103 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 104 through 123 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 16 through 49 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 50 through 77 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 78 through 122 )	B
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 16 through 36 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 37 through 50 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 51 through 64 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 65 through 76 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 77 through 112 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 113 through 123 )	C
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 16 through 36 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 37 through 43 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 44 through 50 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 51 through 64 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 65 through 76 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 77 through 93 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 94 through 103 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 104 through 112 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 113 through 123 )	D

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