PDB-5j4e: Crystal structures reveal signaling states of a short blue light ...

ID or keywords:

Entry

Database: PDB / ID: 5j4e

Title

Crystal structures reveal signaling states of a short blue light photoreceptor protein PpSB1-LOV (Photoexcited state)

Components

Sensory box protein

Keywords

SIGNALING PROTEIN /

LOV domain

Function / homology

Function and homology information

nucleotide binding
Similarity search - Function

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.67 Å

Authors

Granzin, J. / Batra-Safferling, R.

Funding support

Germany, 1items

Citation

Journal: J.Mol.Biol. / Year: 2016
Title: Signaling States of a Short Blue-Light Photoreceptor Protein PpSB1-LOV Revealed from Crystal Structures and Solution NMR Spectroscopy.
Authors: Rollen, K. / Granzin, J. / Panwalkar, V. / Arinkin, V. / Rani, R. / Hartmann, R. / Krauss, U. / Jaeger, K.E. / Willbold, D. / Batra-Safferling, R.

History

Deposition	Apr 1, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 22, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jun 29, 2016	Group: Database references
Revision 1.2	Sep 28, 2016	Group: Database references
Revision 1.3	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.4	Jan 10, 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

-
Download

PDBx/mmCIF format	5j4e.cif.gz	234.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5j4e.ent.gz	189.2 KB	Display	PDB format
PDBx/mmJSON format	5j4e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j4/5j4e ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j4e	HTTPS FTP

-
Related structure data

Related structure data	5j3wSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5j3w-1 3u74-d 6rlw-4 6gg9-2 6c8v-d 3dn7-d 5j3w-2 1pnf-d 2gcd-2 6gg9-1 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

-
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

76.3 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
38.1 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
38.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.409, 71.080, 91.369
Angle α, β, γ (deg.)	90.00, 91.02, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Sensory box protein / LOV protein Mass: 18617.830 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: PP_4629 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88E39
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na-cacodylate, MgCl2, PEG 3000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2014
Radiation	Monochromator: Silicon (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.96863 Å / Relative weight: 1
Reflection	Resolution: 2.67→45.68 Å / Num. obs: 18700 / % possible obs: 99.5 % / Redundancy: 5.6 % / R_merge(I) obs: 0.048 / Net I/σ(I): 17.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5J3W

5j3w

Resolution: 2.67→45.677 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.8

	R_factor	Num. reflection	% reflection
R_free	0.2608	956	5.14 %
R_work	0.186	-	-
obs	0.1898	18604	98.85 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.67→45.677 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4035	0	124	0	4159

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4222
X-RAY DIFFRACTION	f_angle_d	1.383	5742
X-RAY DIFFRACTION	f_dihedral_angle_d	17.004	1482
X-RAY DIFFRACTION	f_chiral_restr	0.058	642
X-RAY DIFFRACTION	f_plane_restr	0.007	740

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 (%)
2.6701-2.8109	0.3368	142	0.2657	2429	X-RAY DIFFRACTION	96
2.8109-2.9869	0.3671	132	0.2731	2522	X-RAY DIFFRACTION	99
2.9869-3.2175	0.3665	145	0.2634	2518	X-RAY DIFFRACTION	99
3.2175-3.5412	0.3737	120	0.2226	2507	X-RAY DIFFRACTION	99
3.5412-4.0533	0.2572	155	0.1933	2516	X-RAY DIFFRACTION	100
4.0533-5.1057	0.2027	128	0.1531	2569	X-RAY DIFFRACTION	100
5.1057-45.6839	0.2354	134	0.1666	2587	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	5.8323	-0.0642	4.8781	1.1332	0.1613	7.5807	-0.3847	-0.6244	0.0782	0.4338	-0.0356	0.0383	-0.0829	0.3908	0.2997	0.9846	0.1846	0.0155	0.9279	-0.0115	0.7122	4.4802	-2.0088	25.7005
2	4.7999	0.7025	-1.5923	6.3186	-0.5109	7.5126	-0.7226	-1.3977	-0.2	1.4769	0.0622	-0.9789	-1.2917	0.9926	0.6121	1.1806	0.1385	-0.1981	1.3628	0.0575	1.0744	18.5955	-4.5499	28.7072
3	6.0372	0.4366	-1.1932	9.5733	-0.6526	6.3223	-0.0724	-0.4958	-0.0361	0.4845	-0.0459	-0.3295	0.7347	0.9173	0.1903	0.6492	0.1153	0.0313	0.9193	0.0893	0.78	12.9386	-8.8604	24.815
4	3.873	0.9711	0.7154	2.3675	-2.2083	5.4555	-1.2986	-1.3794	-1.6045	1.1758	0.4001	-1.3178	0.4375	-1.9493	0.814	1.1936	0.2819	0.1666	1.3658	0.4026	1.0977	10.8887	-17.7389	33.3235
5	3.8633	1.8744	-2.3366	1.8838	-4.3729	2.0077	0.2608	-0.5289	-0.5031	0.9857	-0.871	0.004	-1.6308	2.0742	-0.2247	1.0372	0.2379	0.3765	1.1507	-0.4639	1.7582	18.3434	-6.8839	26.2224
6	8.502	2.7599	0.5689	6.7807	3.9273	3.513	-0.1235	-1.1267	0.3314	0.1435	-0.1956	0.5745	0.0025	-0.1571	0.15	0.6322	0.0848	-0.0815	0.7304	0.1146	0.6942	22.9558	-27.9821	1.4627
7	0.3363	-1.4378	-1.0138	8.8951	7.8434	2.0666	-0.7189	-0.0439	1.7461	-1.4425	2.184	-1.0542	-0.8298	4.37	-0.576	1.0453	0.1829	-0.1546	0.6825	0.1214	0.6762	36.8307	-24.276	-1.8189
8	7.7832	-0.0749	0.5932	4.2158	0.0062	3.9912	-0.0814	0.7112	1.0333	-1.0322	-0.174	0.6833	-1.4944	-1.0045	0.1957	1.0108	0.1952	-0.0113	0.6918	0.1181	0.9905	29.3519	-15.8312	5.3507
9	6.4719	-2.3229	4.0076	3.923	-1.1703	3.3935	0.7696	1.3268	0.6713	0.8014	-0.3829	-0.8261	0.3555	3.1347	-0.6395	0.8506	0.0437	0.0133	0.9957	0.0019	1.3984	42.3976	-20.3926	7.2851
10	4.4787	1.5002	-1.0152	4.5692	-3.2976	6.1069	-0.7917	1.0367	2.2105	-0.6936	-0.1742	-1.9981	0.7451	2.3298	1.054	0.7315	0.1046	0.0132	1.1926	0.1955	1.5659	44.8647	-32.6261	7.565
11	6.1643	1.0798	1.9748	0.2264	-0.2417	4.7045	-0.1753	-1.0361	-0.7807	0.2568	-0.1391	0.8674	0.2748	0.6859	-0.1978	0.7673	0.238	-0.0276	0.8753	0.011	0.9171	39.6333	-30.2457	11.2278
12	3.9755	0.3685	1.4922	3.3752	-1.5706	9.201	-0.2211	-1.1907	0.2311	0.9661	0.2132	-0.7413	-0.6665	-0.4156	-0.3683	0.6174	0.2297	-0.1273	0.9255	-0.16	0.8761	34.7749	-24.2252	10.1142
13	2.5971	0.258	-1.4522	8.2634	2.0908	2.1674	-0.0218	-0.2434	0.3902	-0.5265	0.7411	-0.8875	-0.4294	-0.6473	-0.7594	0.3973	0.0469	-0.092	0.8091	-0.0975	0.7367	32.056	-31.3243	0.2099
14	3.7905	0.1791	-2.5804	5.927	-2.0957	9.3619	0.0378	-1.8915	0.129	0.4838	-1.9564	-0.5747	-3.2316	-2.3517	1.9283	1.4905	0.0129	-0.1299	1.473	-0.0407	0.9105	34.0622	-22.2374	32.4413
15	4.3988	-1.1068	-4.0272	3.3754	-0.9377	5.5349	1.4475	-1.0622	0.6535	-0.4726	-0.7253	0.6568	-0.5792	2.5521	-0.8289	0.8677	0.0189	-0.1652	1.4396	0.0263	1.2194	40.6282	-25.702	6.1736
16	1.5273	0.2521	0.389	2.4733	0.1995	1.9158	-0.0529	-0.6012	0.364	0.3089	0.0709	0.0327	-0.2816	-0.6528	0.0004	0.9496	0.2616	0.028	1.243	0.078	0.9275	-3.4962	-6.5354	20.9407
17	1.1497	0.0957	1.6628	0.9502	-0.398	1.6217	0.3712	-0.9539	-0.7132	-0.3658	-0.7605	0.4851	0.6691	-1.414	-0.0027	1.004	0.0484	0.0539	1.6373	0.0351	1.1229	-12.3465	-16.626	20.6619
18	0.3016	-0.1893	-0.2262	0.6149	0.4982	0.9468	0.5992	-0.7514	-0.7685	-0.5041	-1.1351	1.3076	1.2643	-2.3794	-0.0011	1.6228	-0.1075	0.0118	2.9623	0.1912	1.3214	-18.241	-17.9437	31.3173
19	2.2158	-0.7273	0.3989	0.6862	-1.1473	1.4473	-0.5942	-1.3308	-0.8433	0.7252	0.2229	1.1553	0.3935	-0.8001	0.0002	1.1447	0.2174	0.1119	1.5343	0.3908	1.1495	-10.3488	-18.6094	32.8595
20	2.7599	1.3476	1.1613	1.9089	2.8185	4.4752	0.2876	-0.2008	-1.7964	0.1451	0.2726	2.1688	0.2562	-0.0924	0.0039	1.0293	0.0958	0.4347	1.6783	0.2257	0.9114	-4.7052	-17.5593	34.6647
21	0.1068	0.03	-0.0343	0.1077	0.0414	0.0398	0.6636	0.0746	0.6522	0.492	0.8238	0.7886	-0.1328	-0.2073	-0.0007	1.3259	0.6366	-0.0598	3.7935	0.0142	1.6109	-16.8137	-16.6174	31.0681
22	4.962	0.1799	-2.0961	3.2541	1.437	4.2986	0.2683	0.5794	-0.7855	-0.1766	0.1902	0.1529	-0.0149	0.3785	-0.2614	0.704	0.1102	-0.1247	0.7796	-0.004	0.8206	18.7511	-33.0102	3.4291
23	6.6468	0.0428	3.7224	0.8417	1.3843	2.9033	0.1494	-1.3	-0.8216	0.1347	0.3476	0.3794	0.4016	-0.3125	-0.4119	0.7641	0.0018	-0.0222	0.3691	0.1615	0.9428	11.5132	-37.725	12.3464
24	4.1117	-0.3959	1.4293	6.6635	-1.5986	7.8545	0.4401	-0.8648	-0.7977	0.1184	-0.2758	0.3489	0.935	-0.8515	-0.1588	0.8358	0.0457	-0.0223	0.7122	0.2923	0.8683	5.8958	-33.9038	18.9311
25	2.6099	-0.1177	-0.3406	3.5437	1.821	5.0691	-0.403	-0.5355	-0.3507	0.6383	0.4669	-0.1096	0.0127	0.5812	0.041	0.7251	0.1493	-0.0145	0.844	0.1318	0.8228	12.7804	-29.6568	19.809
26	4.2533	2.5425	0.8456	4.6278	1.6222	5.2335	0.1182	0.3565	-0.0361	-0.1493	0.3413	0.2008	0.8082	0.8079	-0.1485	0.6829	0.1399	0.088	0.4797	0.1425	0.7588	9.6315	-29.5978	5.896
27	1.1313	0.0504	-0.4509	0.4594	-0.9519	1.8796	0.0843	0.9983	0.5166	1.2928	1.2095	-0.9893	-0.5714	1.8273	0.34	1.2265	0.1107	-0.2951	1.3351	0.1231	0.9281	25.4466	-24.0441	35.2549
28	4.2888	2.7278	-3.142	1.8649	-0.9504	9.1311	2.6102	-0.3602	0.7891	-0.5421	-1.4193	0.1713	1.8933	0.0546	-0.7957	0.9991	0.093	-0.0094	0.4599	0.0292	0.74	6.1481	-31.6366	17.7074

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 41 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 42 through 74 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 75 through 109 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 110 through 133 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 500 through 500 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 24 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 25 through 33 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 34 through 48 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 49 through 64 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 65 through 74 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 75 through 86 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 87 through 104 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 105 through 119 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 120 through 134 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 500 through 500 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 24 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 25 through 48 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 49 through 74 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 75 through 102 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 103 through 134 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 500 through 500 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1 through 24 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 25 through 41 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 42 through 75 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 76 through 103 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 104 through 119 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 120 through 134 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 500 through 500 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi