PDB-6gay: A fast recovering full-length LOV protein (DsLOV) from the marine...

ID or keywords:

Entry

Database: PDB / ID: 6gay

Title

A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - M49I mutant

Components

Putative blue-light photoreceptor

Keywords

SIGNALING PROTEIN / LIGHT-OXYGEN-VOLTAGE / LOV / PAS

Function / homology

Function and homology information

PAS-associated, C-terminal / PAC domain profile. /

PAS domain /

Beta-Lactamase / PAS repeat profile. /

PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology

Biological species

Dinoroseobacter shibae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.86 Å

Authors

Granzin, J. / Batra-Safferling, R. / Roellen, K.

Citation

Journal: Biochemistry / Year: 2018
Title: Mechanistic Basis of the Fast Dark Recovery of the Short LOV Protein DsLOV from Dinoroseobacter shibae.
Authors: Fettweiss, T. / Rollen, K. / Granzin, J. / Reiners, O. / Endres, S. / Drepper, T. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R. / Krauss, U.

History

Deposition	Apr 13, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6gay.cif.gz	112.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6gay.ent.gz	87 KB	Display	PDB format
PDBx/mmJSON format	6gay.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/ga/6gay ftp://data.pdbj.org/pub/pdb/validation_reports/ga/6gay	HTTPS FTP

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Related structure data

Related structure data	6gb3C 6gbaC 6gbvC 4kukS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1kme-2 1tn0-2 3har-d 1s51-1 1xji-d 1vjm-d 3haq-d 3han-d 1s51-2 1s53-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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 (3) #207 - Mar 2017 Photoactive Yellow Protein similarity (3)

Deposited unit

A: Putative blue-light photoreceptor

B: Putative blue-light photoreceptor

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	56.675, 56.675, 156.383
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-674- HOH

#1: Protein	Putative blue-light photoreceptor Mass: 16842.883 Da / Num. of mol.: 2 / Mutation: M49I Source method: isolated from a genetically manipulated source Details: C-terminal hexa-histidine-tagged fusion proteins (tag sequence: LEHHHHHH) in E. coli BL21(DE3) Source: (gene. exp.) Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12) (bacteria) Strain: DSM 16493 / NCIMB 14021 / DFL 12 / Gene: Dshi_2006 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A8LP63
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.86 Å³/Da / Density % sol: 33.8 % / Description: tetragonal plates
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M Na-acetate, 0.1 M Ammonium sulfate, 0.3 M Sodium formate, 3 % PGA-LM, 5 % (w/v) PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.86→45.89 Å / Num. obs: 22330 / % possible obs: 99.9 % / Redundancy: 9.2 % / B_iso Wilson estimate: 26.3 Å² / R_merge(I) obs: 0.061 / R_rim(I) all: 0.065 / Net I/σ(I): 23.2
Reflection shell	Resolution: 1.86→1.9 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1358 / CC_1/2: 0.894 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1-2155_1692: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4KUK

4kuk

Resolution: 1.86→45.889 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2092	1138	5.11 %
R_work	0.1657	-	-
obs	0.1679	22251	99.74 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.86→45.889 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1724	0	72	135	1931

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	1909
X-RAY DIFFRACTION	f_angle_d	1.624	2624
X-RAY DIFFRACTION	f_dihedral_angle_d	16.428	1146
X-RAY DIFFRACTION	f_chiral_restr	0.102	282
X-RAY DIFFRACTION	f_plane_restr	0.012	343

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 (%)
1.86-1.9447	0.2721	133	0.2254	2578	X-RAY DIFFRACTION	99
1.9447-2.0472	0.2655	138	0.2035	2570	X-RAY DIFFRACTION	100
2.0472-2.1755	0.2297	157	0.1822	2588	X-RAY DIFFRACTION	100
2.1755-2.3434	0.2298	146	0.1701	2585	X-RAY DIFFRACTION	100
2.3434-2.5792	0.2397	135	0.1867	2634	X-RAY DIFFRACTION	100
2.5792-2.9524	0.2312	142	0.1884	2621	X-RAY DIFFRACTION	100
2.9524-3.7194	0.1978	137	0.1545	2692	X-RAY DIFFRACTION	100
3.7194-45.9025	0.1774	150	0.1443	2845	X-RAY DIFFRACTION	100

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	4.2459	-2.1439	1.4911	2.4866	0.6541	2.7944	0.1746	0.1713	1.019	-0.0703	0.1328	0.8893	-0.2969	-0.6968	-0.4054	0.2997	0.0501	0.0096	0.3713	-0.0112	0.4353	-10.9456	-5.0429	-13.732
2	7.0549	-5.5276	-0.4293	9.7386	-5.239	7.0592	-0.0679	0.0409	0.1583	-0.2818	-0.0895	-0.8355	-0.0883	0.2496	0.1523	0.2326	-0.0298	0.0288	0.3015	-0.0187	0.2947	5.0071	-4.4615	-19.042
3	4.5028	3.2592	-6.0037	8.2141	-4.1293	8.2926	0.2667	-0.196	0.5333	0.0914	-0.1919	0.3131	-0.7114	-0.233	-0.0151	0.2201	0.0124	-0.0199	0.2107	-0.0425	0.1977	-3.9933	-3.9193	-10.8876
4	4.8713	-5.0996	-3.8658	8.9381	1.8631	8.3688	-0.0148	-0.0019	0.0922	-0.0634	0.2145	0.0099	0.1964	-0.254	-0.2676	0.2139	0.0301	-0.0058	0.3066	-0.005	0.2084	-11.3684	-10.725	-6.4964
5	3.6124	1.2206	-1.1629	0.4494	-0.2598	1.4863	0.0169	-0.3421	-0.2996	0.1783	-0.0901	-0.0999	-0.0218	0.2017	0.113	0.2705	0.0347	-0.0433	0.2535	0.0151	0.2843	-1.5201	-12.1749	-8.9215
6	0.6921	0.0998	0.4811	3.5924	-2.2026	4.9568	0.0535	0.0479	-0.0906	-0.1133	0.049	-0.0805	0.2079	0.1719	-0.0817	0.1832	0.0165	-0.0065	0.2426	-0.0402	0.2337	-5.9861	-16.9943	-21.7033
7	7.0066	5.7775	-1.7083	4.7814	-1.5199	2.4024	-0.0489	0.1717	0.3595	-0.1058	0.1079	0.519	-0.0655	-0.0992	0.0272	0.2159	0.0392	-0.0058	0.2224	-0.0167	0.1899	-11.1169	-9.0747	-20.7269
8	1.9964	-3.202	0.4698	5.8211	-2.3016	3.6075	0.5759	0.1947	2.5989	-0.1386	0.2809	0.853	-1.4961	0.2828	-0.7464	0.5861	-0.0818	0.0774	0.3356	0.067	0.7027	-2.932	9.6442	-25.8094
9	8.433	7.3572	-4.9034	7.6585	-5.8456	7.045	0.4371	-0.3991	0.2022	0.349	-0.4458	0.1342	-0.2551	0.1744	-0.0121	0.1604	0.0426	-0.0056	0.1766	-0.0245	0.1813	-10.1307	-9.8624	-17.7418
10	3.523	-0.7544	-4.6126	2.1901	0.8847	6.5789	-0.1022	0.3663	-0.0101	-0.0481	0.6646	-0.4755	0.6901	1.0302	-0.4668	0.2366	0.0146	0.0012	0.3274	-0.1016	0.3021	-2.8189	-13.3146	-19.7363
11	6.0207	-1.6596	1.4941	8.9302	-4.6114	7.3791	-0.1943	0.3304	-0.3248	-0.3807	0.2211	0.0143	0.4004	0.0872	0.0183	0.3265	-0.065	-0.0193	0.3512	-0.096	0.3059	-19.8308	-21.2072	-41.9003
12	5.0164	4.9246	-6.4598	6.5553	-6.7441	8.7413	-0.3304	1.43	1.2278	0.0413	0.2681	0.4748	-0.6869	0.1338	-0.0363	0.3649	-0.1204	-0.0627	0.3878	0.0925	0.3629	-24.1745	-9.3251	-46.1904
13	8.9686	-4.7321	8.1374	7.8815	-5.1785	7.5997	0.3104	1.2989	0.2235	-0.883	-0.0957	0.0306	1.0613	0.4219	-0.1722	0.4729	-0.1352	0.0358	0.6591	-0.0182	0.276	-19.3268	-16.6337	-51.3961
14	2.3739	1.5012	-0.4661	1.8273	-2.488	5.6924	-0.0714	0.3769	-0.021	-0.188	-0.0185	-0.1811	0.0766	0.3362	0.0843	0.2561	0.0248	0.059	0.3878	-0.0536	0.2428	-6.7444	-14.1093	-39.1993
15	3.1977	0.5782	-0.5302	4.0641	-1.3086	4.3299	0.0062	0.142	-0.0871	-0.0645	0.1723	0.1458	0.1245	0.0517	-0.1602	0.1536	0.0108	-0.0078	0.206	-0.0294	0.1889	-16.1	-14.7883	-35.6543
16	6.9562	-2.0568	0.6114	3.7225	-1.2632	8.4278	-0.0986	0.2199	0.1201	-0.8681	0.1533	-0.1885	-0.1422	-0.0787	-0.085	0.211	0.0084	-0.0182	0.2876	-0.0298	0.2128	-18.5249	-13.7726	-37.0848
17	8.9657	-0.0452	2.4535	9.043	-0.8743	7.9904	-0.2994	0.8889	-0.0364	-0.2727	-0.0482	-0.1877	0.4361	0.1078	0.2895	0.2626	-0.0589	0.0133	0.4036	-0.0711	0.2544	-11.3322	-16.7974	-40.2354

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 32 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 47 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 48 through 53 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 54 through 60 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 75 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 76 through 110 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 111 through 122 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 123 through 127 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 128 through 141 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 500 through 500 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 34 through 53 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 54 through 60 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 61 through 71 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 72 through 93 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 94 through 127 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 128 through 141 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 500 through 500 )

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