PDB-6gg9: Crystal structures of a short blue light photoreceptor protein Pp...

ID or keywords:

Entry

Database: PDB / ID: 6gg9

Title

Crystal structures of a short blue light photoreceptor protein PpSB1-LOV mutant (dark state) - R61H/R66I

Components

Sensory box protein

Keywords

SIGNALING PROTEIN / blue light photoreceptor / Sensory box protein

Function / homology

Function and homology information

PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain ...
Similarity search - Domain/homology

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.04 Å

Authors

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

Citation

Journal: PLoS One / Year: 2018
Title: Small-angle X-ray scattering study of the kinetics of light-dark transition in a LOV protein.
Authors: Katrin Röllen / Joachim Granzin / Renu Batra-Safferling / Andreas Maximilian Stadler /

Abstract: Light, oxygen, voltage (LOV) photoreceptors consist of conserved photo-responsive domains in bacteria, archaea, plants and fungi, and detect blue-light via a flavin cofactor. We investigated the blue- ...

History

Deposition	May 3, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 25, 2018	Provider: repository / Type: Initial release
Revision 1.1	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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Download

PDBx/mmCIF format	6gg9.cif.gz	239.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6gg9.ent.gz	192.6 KB	Display	PDB format
PDBx/mmJSON format	6gg9.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/gg/6gg9 ftp://data.pdbj.org/pub/pdb/validation_reports/gg/6gg9	HTTPS FTP

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Related structure data

Related structure data	SASDDE6C SASDDG6C 5j3wS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1ixk-d 5j3w-1 6q8e-d 1td6-d 6fte-d 5j3w-2 4k5b-2 4dqn-d 7l26-2 5j4e-2 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 - 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 (5) #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: Sensory box protein

B: Sensory box protein

C: Sensory box protein

D: Sensory box protein

hetero molecules

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

1

A: Sensory box protein

C: Sensory box protein

hetero molecules

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

2

B: Sensory box protein

D: Sensory box protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	102.700, 76.506, 83.279
Angle α, β, γ (deg.)	90.00, 106.23, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Sensory box protein Mass: 18554.746 Da / Num. of mol.: 4 / Mutation: R61H, R66I Source method: isolated from a genetically manipulated source Details: expression tag: MGSSHHHHHHSSGLVPRGSH / Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: PP_4629 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q88E39
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.12 Å³/Da / Density % sol: 42.12 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.2 MgCl2, 0.1M MES, 15% (w/v) PEG4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9772 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9772 Å / Relative weight: 1
Reflection	Resolution: 2.04→48.45 Å / Num. obs: 39334 / % possible obs: 99.5 % / Redundancy: 4.4 % / B_iso Wilson estimate: 37.5 Å² / R_merge(I) obs: 0.069 / R_rim(I) all: 0.078 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.04→2.1 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3076 / % possible all: 99.7

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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: 5J3W

5j3w

Resolution: 2.04→48.45 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.27

	R_factor	Num. reflection	% reflection
R_free	0.2367	1955	4.98 %
R_work	0.1947	-	-
obs	0.1968	39265	99.27 %

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å

Refinement step

Cycle: LAST / Resolution: 2.04→48.45 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4165	0	124	110	4399

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4373
X-RAY DIFFRACTION	f_angle_d	0.928	5941
X-RAY DIFFRACTION	f_dihedral_angle_d	14.713	2596
X-RAY DIFFRACTION	f_chiral_restr	0.055	652
X-RAY DIFFRACTION	f_plane_restr	0.006	770

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 (%)
2.04-2.091	0.3581	156	0.3036	2648	X-RAY DIFFRACTION	99
2.091-2.1476	0.3588	147	0.2962	2629	X-RAY DIFFRACTION	99
2.1476-2.2108	0.3041	126	0.282	2661	X-RAY DIFFRACTION	99
2.2108-2.2821	0.3107	131	0.2612	2624	X-RAY DIFFRACTION	98
2.2821-2.3637	0.3081	148	0.2336	2665	X-RAY DIFFRACTION	100
2.3637-2.4583	0.2847	128	0.2394	2675	X-RAY DIFFRACTION	99
2.4583-2.5702	0.2596	128	0.2253	2673	X-RAY DIFFRACTION	99
2.5702-2.7057	0.2751	124	0.2199	2631	X-RAY DIFFRACTION	99
2.7057-2.8752	0.2696	149	0.2308	2645	X-RAY DIFFRACTION	99
2.8752-3.0971	0.274	148	0.2302	2677	X-RAY DIFFRACTION	100
3.0971-3.4087	0.2584	149	0.1998	2675	X-RAY DIFFRACTION	100
3.4087-3.9018	0.1972	144	0.1719	2662	X-RAY DIFFRACTION	99
3.9018-4.9151	0.1852	138	0.1431	2712	X-RAY DIFFRACTION	100
4.9151-48.4636	0.1948	139	0.1635	2733	X-RAY DIFFRACTION	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	0.4892	-0.1412	-0.4615	1.9958	0.9979	0.7204	-0.3595	0.2319	0.2283	-0.2314	0.5688	0.7074	-0.9802	-0.8965	0.0001	0.4686	0.0602	-0.0276	0.5527	0.0742	0.5076	-9.3895	1.0443	20.5138
2	1.3144	-0.7976	0.7568	0.9664	0.2545	1.3014	0.3732	-0.208	0.3179	0.2296	-0.4029	-0.1389	-0.3896	0.5965	0.0016	0.393	-0.0093	-0.0203	0.3875	0.0637	0.3669	8.5616	-2.7201	23.2945
3	0.0299	0.0734	0.0859	0.5211	-0.0445	0.5364	0.2327	-0.528	0.5195	0.2991	0.0012	-0.6386	-0.0636	1.2835	0.0008	0.4678	0.0263	-0.0613	0.5695	0.034	0.4694	14.7165	0.6528	22.6957
4	2.0077	0.1426	-0.625	0.2514	-0.2043	0.2945	0.0478	-1.6171	0.2831	0.8868	-0.516	0.2702	-0.9956	-0.0707	-0.0124	0.4611	-0.0204	0.0249	0.3944	-0.0471	0.3737	5.5046	-3.6998	33.923
5	0.8603	0.053	-0.0215	0.7684	-0.2478	1.4652	0.2696	-0.8316	0.2024	0.2485	-0.5033	-0.1433	-1.0999	1.0038	-0.0136	0.6224	-0.1051	-0.0361	0.5803	-0.067	0.4994	14.2385	0.2156	30.895
6	0.0056	0.0132	0.0029	0.1242	0.0612	-0.0007	0.0189	-0.0245	-0.5176	-0.3155	0.0172	-0.8962	-1.076	0.714	-0.0023	0.9123	0.0681	-0.1554	1.3573	-0.0057	1.0398	23.33	-13.3124	31.5045
7	0.271	0.7411	0.2622	2.0487	0.6493	0.5239	-0.6381	1.733	-0.7765	-1.0999	1.0084	-1.3484	0.8269	1.2129	0.027	0.4964	-0.0019	0.1256	1.1056	-0.2043	0.8831	19.4298	-13.6581	19.0786
8	4.4732	0.2591	-0.554	3.2702	-0.3057	1.3634	0.0167	-0.0468	-0.6409	0.0476	-0.0091	-0.28	0.3106	0.6229	-0.0004	0.4312	0.0575	-0.0294	0.5039	-0.0013	0.4125	12.1216	-11.6495	26.0168
9	1.7759	0.1494	0.4403	0.7774	0.6704	0.6927	-0.1513	0.5945	0.1128	0.3061	0.5043	0.103	-0.3762	-0.2248	0.009	0.3384	-0.0116	-0.0369	0.429	0.1257	0.2832	8.299	-3.0078	17.6651
10	0.3996	0.0247	-0.7114	-0.0033	-0.0823	1.2607	-0.0216	-1.312	-1.6906	1.5488	0.6752	-1.2953	0.9306	0.6897	0.4742	0.9432	0.0702	-0.1748	0.558	0.3985	0.9982	6.9201	-27.4013	38.3391
11	1.2037	1.5567	1.0592	2.0042	1.3636	0.9353	-0.049	1.0836	-0.0358	0.5629	0.6146	-2.0501	-0.7204	1.9611	0.1173	0.4914	0.0826	0.001	0.6936	-0.0004	0.5048	17.1207	-7.8531	24.4088
12	1.0273	-0.7826	0.3288	0.5839	-0.411	0.6892	0.2575	1.0338	0.3143	0.1868	-0.0884	0.6373	-0.007	-1.1862	0.0001	0.4185	0.0297	-0.0037	0.6144	-0.0472	0.4926	15.6201	-29.9847	0.1889
13	0.9777	0.1277	0.815	3.1138	1.0742	1.4462	0.4353	0.111	0.948	-0.384	0.1513	-0.2509	-0.6328	0.3299	-0.0002	0.4374	0.0151	0.0137	0.4594	-0.0729	0.4765	31.313	-22.9871	2.5827
14	0.4597	0.0075	-0.4608	1.238	0.4919	0.744	0.6844	-0.2056	0.976	-0.8372	0.2833	-0.6039	-1.0574	0.5683	0.0152	0.7597	0.0378	0.1562	0.6137	-0.0926	0.897	35.1433	-16.8489	1.9143
15	0.1294	-0.3709	-0.4236	2.4049	0.5108	1.3633	0.6542	0.0819	1.0752	-0.846	-1.0117	-0.8748	-0.6845	0.7388	-0.0009	0.56	0.0845	-0.0079	1.163	-0.1601	0.8759	45.6582	-27.3689	9.9729
16	4.931	-0.804	-1.971	1.886	1.1307	4.6698	-0.1547	-0.6978	0.337	0.1457	0.3132	-0.4752	0.1304	0.6269	0.0037	0.4222	0.1424	-0.024	0.5904	-0.1021	0.4193	35.1604	-27.8858	7.0836
17	0.4121	0.2345	0.1382	1.0634	-0.3867	0.4645	0.405	-0.6671	0.1094	0.1887	-0.0327	-0.4736	-0.198	1.2099	-0.0307	0.9465	0.255	-0.2465	1.0486	-0.1724	0.69	33.7602	-21.068	32.6902
18	0.0938	-0.005	0.03	0.0986	0.0906	0.0916	1.0852	-1.1636	0.9164	-0.4433	0.4482	-2.5148	-0.8942	1.1735	-0.002	0.6719	-0.0078	0.2272	0.8903	-0.3361	1.0011	40.6306	-25.0124	5.8478
19	2.1893	-0.1785	1.0668	1.8833	-0.0618	3.1209	-0.2236	0.5373	0.1749	-0.2306	0.0796	0.1048	0.033	-0.1071	-0.0004	0.3652	0.0263	-0.0194	0.4323	0.0665	0.3848	-5.018	-3.6106	19.5445
20	1.1728	0.8561	0.7044	1.0237	-0.1213	1.3404	-0.6154	0.6041	-0.7257	0.1348	0.4201	0.733	0.1354	-0.5381	-0.001	0.4457	0.0032	0.0364	0.6077	0.0066	0.5125	-13.9391	-11.4045	20.261
21	0.1146	-0.1357	-0.0464	1.0388	0.5136	0.2345	-0.3286	0.6988	-0.2621	-0.3091	0.5024	1.3377	-0.2203	-0.4931	-0.001	0.691	-0.107	-0.0256	1.0165	-0.0051	0.7667	-18.2108	-14.5112	18.4213
22	0.0271	0.0424	0.0566	0.0328	0.0733	0.105	-0.1871	0.3125	0.1032	-0.4604	-0.2806	0.7263	-0.1105	-2.2025	-0.0035	1.1341	-0.3465	0.0591	1.2037	-0.0406	0.9114	-22.5364	-22.2477	31.9429
23	4.3463	1.6776	-1.0735	2.5316	-1.5553	6.7032	-0.0695	-0.0651	0.1543	0.6253	-0.0008	0.4467	-0.0654	-0.5082	0.0108	0.4078	-0.0011	0.0665	0.4125	-0.0534	0.5231	-14.5267	-10.5405	30.7254
24	0.9237	-0.2031	-0.5044	0.1508	-0.041	0.8397	-0.2328	-1.7232	-0.9178	0.3309	0.2448	-0.1028	0.278	-0.4754	0.0446	0.9713	0.1471	0.0972	0.7676	0.1453	1.1392	-3.2445	-29.3356	39.3276
25	1.2006	-0.6621	3.1514	3.2224	-0.4976	8.7854	0.3729	0.1062	-0.5197	0.0393	-0.3369	0.8536	1.065	-1.0542	0.5029	0.4476	0.0405	-0.0022	0.0964	-0.0743	0.389	-19.3024	-12.2197	28.8206
26	0.6654	-0.2837	0.1645	0.985	0.7446	0.7605	-0.2333	0.7346	-0.0854	-0.3581	-0.1652	-0.2077	0.0926	0.1643	-0.0005	0.4325	0.0373	0.0737	0.5917	-0.0972	0.5373	24.2987	-33.4517	-1.0039
27	1.1912	0.3603	-0.2583	3.5153	-0.9971	2.5399	-0.1845	-0.3982	-0.6493	-0.0267	0.0403	0.0143	0.3263	-0.2899	0.0026	0.4519	0.0714	0.0397	0.4574	-0.018	0.4367	12.4069	-36.4702	11.3888
28	0.5186	0.1201	0.214	0.6375	-0.4022	0.3851	0.0153	-0.454	-1.0794	-0.0084	-0.1705	0.2793	0.7571	-0.4458	-0.002	0.6091	0.0301	0.0763	0.5242	0.0014	0.719	9.4214	-41.9193	15.6494
29	2.2234	1.3527	-0.3826	2.6519	1.1341	1.027	0.223	-0.7356	0.4341	0.7608	0.0349	1.1904	-0.2934	-0.2275	0.001	0.549	0.0967	0.147	0.6414	-0.0657	0.7689	6.3583	-27.5098	21.4697
30	2.4842	0.2239	-0.6013	1.7935	1.2943	1.4315	-0.2749	-0.4426	-0.2145	0.4255	0.1484	0.0417	-0.1661	-0.2903	-0.0002	0.3324	0.0856	-0.0098	0.4457	0.0322	0.4528	13.9056	-32.4107	17.8032
31	0.7925	0.0447	-0.0804	0.7281	-0.1648	0.3294	0.1889	0.5094	-0.0561	0.0326	0.1646	0.1084	0.1023	0.2497	0.0003	0.3751	0.0288	-0.0379	0.4584	-0.0309	0.5024	9.7879	-30.2438	6.1709
32	0.6764	0.1137	-0.6343	0.8531	0.5252	0.9798	-0.6357	-1.48	0.6802	-0.4824	0.5769	-0.9373	-1.8044	-0.079	0.0545	1.0627	0.011	-0.2399	1.0111	0.0458	0.484	24.3135	-22.3688	34.9442
33	0.4481	-0.0577	0.0749	0.0878	-0.0797	0.0622	-0.1064	-0.8805	-0.5074	0.4538	-0.2708	1.2911	0.9591	-0.6976	0.0058	0.4543	0.0112	0.0532	0.5279	-0.0261	0.4604	6.2295	-32.2369	17.5746

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 13 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 14 through 24 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 25 through 33 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 34 through 41 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 42 through 57 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 58 through 63 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 64 through 74 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 75 through 104 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 105 through 119 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 120 through 132 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 500 through 500 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 1 through 12 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 13 through 41 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 42 through 57 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 58 through 74 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 75 through 119 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 120 through 135 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 500 through 500 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 1 through 24 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 25 through 41 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 42 through 57 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 58 through 63 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 64 through 119 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 120 through 134 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 500 through 500 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 1 through 13 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 14 through 41 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 42 through 57 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 58 through 86 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 87 through 104 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 105 through 119 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 120 through 135 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 500 through 500 )

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