PDB-6hmj: Structure of an RNA-binding Light-Oxygen-Voltage Receptor

ID or keywords:

Entry

Database: PDB / ID: 6hmj

Title

Structure of an RNA-binding Light-Oxygen-Voltage Receptor

Components

Putative PAS/PAC sensor protein

Keywords

SIGNALING PROTEIN / sensory photoreceptor / light-oxygen-voltage / RNA binding

Function / homology

Function and homology information

Biological species

Nakamurella multipartita DSM 44233 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.51 Å

Authors

Ziegler, T. / Moniot, S. / Moeglich, A.

Funding support

Germany, 1items

Citation

Journal: Nat.Chem.Biol. / Year: 2019
Title: A blue light receptor that mediates RNA binding and translational regulation.
Authors: Weber, A.M. / Kaiser, J. / Ziegler, T. / Pilsl, S. / Renzl, C. / Sixt, L. / Pietruschka, G. / Moniot, S. / Kakoti, A. / Juraschitz, M. / Schrottke, S. / Lledo Bryant, L. / Steegborn, C. / ...

History

Deposition	Sep 12, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 28, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 15, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6hmj.cif.gz	786 KB	Display	PDBx/mmCIF format
PDB format	pdb6hmj.ent.gz	674 KB	Display	PDB format
PDBx/mmJSON format	6hmj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6hmj_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6hmj_full_validation.pdf.gz	1.7 MB	Display
Data in XML	6hmj_validation.xml.gz	50.8 KB	Display
Data in CIF	6hmj_validation.cif.gz	68.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/6hmj ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hmj	HTTPS FTP

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Related structure data

Similar structure data	4gay-d 2zjs-d 6c5r-2 6d11-d 5lc4-d 1hqc-d 4gzu-d 2or9-d 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

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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) #190 - Oct 2015 Two-component Systems similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

PDB pages

PDBj /

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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)
#190 - Oct 2015
Two-component Systems
similarity (1)
#97 - Jan 2008
Circadian Clock Proteins
similarity (1)
#134 - Feb 2011
Integrin
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#194 - Feb 2016
Designer Insulins
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#259 - Jul 2021
Designed Proteins and Citizen Science
similarity (1)

Deposited unit

A: Putative PAS/PAC sensor protein

B: Putative PAS/PAC sensor protein

C: Putative PAS/PAC sensor protein

D: Putative PAS/PAC sensor protein

hetero molecules

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

1

A: Putative PAS/PAC sensor protein

B: Putative PAS/PAC sensor protein

hetero molecules

defined by author&software
Evidence: gel filtration
81.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Putative PAS/PAC sensor protein

D: Putative PAS/PAC sensor protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	67.013, 150.345, 219.783
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Putative PAS/PAC sensor protein Mass: 40421.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nakamurella multipartita DSM 44233 (bacteria) Strain: ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 / Y-104 Gene: Namu_4361 / Production host: Escherichia coli (E. coli) / References: UniProt: C8XJT7

#1: Protein

Putative PAS/PAC sensor protein

Mass: 40421.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Nakamurella multipartita DSM 44233 (bacteria)
Strain: ATCC 700099 / DSM 44233 / CIP 104796 / JCM 9543 / NBRC 105858 / Y-104
Gene: Namu_4361 / Production host:

Escherichia coli (E. coli) / References: UniProt: C8XJT7

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Non-polymers , 5 types, 168 molecules

#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₅N₂
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.42 Å³/Da / Density % sol: 64.07 %
Crystal grow	Temperature: 277.3 K / Method: vapor diffusion, hanging drop Details: 0.1 M bicine, pH 9.2, 15% (w/v) PEG 20,000, 2% dioxane, 0.8 M imidazole acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91814 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91814 Å / Relative weight: 1
Reflection	Resolution: 2.51→71.127 Å / Num. obs: 75981 / % possible obs: 98.69 % / Redundancy: 4.3 % / R_pim(I) all: 0.1082 / R_rim(I) all: 0.2283 / Net I/σ(I): 8
Reflection shell	Resolution: 2.51→2.6 Å / R_pim(I) all: 1.074 / R_rim(I) all: 2.321

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
DIALS		data reduction
Aimless		data scaling
SHELXCD		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.51→71.127 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2541	3748	4.94 %
R_work	0.2431	-	-
obs	0.2437	75886	98.69 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.51→71.127 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10733	0	155	158	11046

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11101
X-RAY DIFFRACTION	f_angle_d	0.634	15148
X-RAY DIFFRACTION	f_dihedral_angle_d	12.155	6608
X-RAY DIFFRACTION	f_chiral_restr	0.041	1764
X-RAY DIFFRACTION	f_plane_restr	0.004	1976

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 (%)
2.51-2.5418	0.4696	139	0.4669	2619	X-RAY DIFFRACTION	99
2.5418-2.5753	0.4455	133	0.4397	2675	X-RAY DIFFRACTION	99
2.5753-2.6105	0.43	138	0.423	2655	X-RAY DIFFRACTION	99
2.6105-2.6478	0.3645	129	0.3857	2662	X-RAY DIFFRACTION	100
2.6478-2.6874	0.3704	148	0.3762	2649	X-RAY DIFFRACTION	99
2.6874-2.7294	0.3215	119	0.3396	2645	X-RAY DIFFRACTION	100
2.7294-2.7741	0.3402	140	0.3392	2661	X-RAY DIFFRACTION	99
2.7741-2.8219	0.3972	135	0.3211	2656	X-RAY DIFFRACTION	99
2.8219-2.8733	0.3535	155	0.3109	2623	X-RAY DIFFRACTION	99
2.8733-2.9285	0.3265	173	0.3075	2641	X-RAY DIFFRACTION	99
2.9285-2.9883	0.3102	120	0.3041	2652	X-RAY DIFFRACTION	100
2.9883-3.0533	0.3707	125	0.3023	2690	X-RAY DIFFRACTION	98
3.0533-3.1243	0.3393	148	0.3137	2628	X-RAY DIFFRACTION	100
3.1243-3.2024	0.305	135	0.3037	2693	X-RAY DIFFRACTION	98
3.2024-3.289	0.305	139	0.2781	2648	X-RAY DIFFRACTION	100
3.289-3.3858	0.2821	133	0.2529	2669	X-RAY DIFFRACTION	98
3.3858-3.4951	0.2667	139	0.2499	2657	X-RAY DIFFRACTION	99
3.4951-3.62	0.2425	130	0.2462	2637	X-RAY DIFFRACTION	98
3.62-3.7649	0.2601	140	0.2429	2687	X-RAY DIFFRACTION	99
3.7649-3.9363	0.2715	138	0.2386	2687	X-RAY DIFFRACTION	99
3.9363-4.1438	0.2185	144	0.2107	2673	X-RAY DIFFRACTION	100
4.1438-4.4033	0.2407	140	0.1889	2705	X-RAY DIFFRACTION	99
4.4033-4.7433	0.2028	137	0.1752	2681	X-RAY DIFFRACTION	98
4.7433-5.2205	0.1747	143	0.1871	2688	X-RAY DIFFRACTION	98
5.2205-5.9756	0.2274	135	0.2106	2711	X-RAY DIFFRACTION	98
5.9756-7.5272	0.2212	158	0.2345	2714	X-RAY DIFFRACTION	97
7.5272-71.1557	0.1823	135	0.1913	2832	X-RAY DIFFRACTION	96

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	8.5148	2.0814	2.7348	6.6117	0.7213	2.8652	-0.1145	0.669	0.1145	-0.8924	-0.0498	-0.1228	-0.4462	0.1428	0.1503	0.8665	0.1826	-0.0168	0.6722	0.0089	0.392	5.8771	78.7107	86.5689
2	1.051	-1.0749	-2.1196	0.5628	1.4966	5.0786	0.0732	0.0284	0.0154	-0.2047	0.0598	-0.0786	-0.0514	0.441	-0.1757	0.5859	-0.0436	0.0325	0.6403	-0.0725	0.5237	-12.7603	93.0474	138.5437
3	1.9976	1.0172	-2.5399	5.0116	-2.5253	7.3944	-0.0325	-0.1428	0.1329	0.3152	0.0374	0.2245	-0.0453	0.2846	-0.0113	0.3326	0.0706	-0.0377	0.5114	-0.0703	0.4915	-21.2886	102.1696	180.0543
4	-0.2917	0.1101	0.5739	2.464	1.9972	4.7614	0.001	0.1837	-0.0526	-0.1663	-0.119	0.3576	-0.1866	-0.6525	0.1632	0.3521	0.0985	-0.0271	0.5104	0.02	0.5794	-27.6219	102.75	163.9345
5	7.8119	3.4152	-4.3878	7.0611	-1.7306	2.6526	-0.1143	-0.0783	1.2956	0.218	-0.1484	-0.9635	-0.9374	0.6626	0.2754	0.892	0.0639	-0.2493	0.7955	0.0748	1.2451	21.3841	92.5374	100.3312
6	8.1807	0.4111	-3.2503	1.2321	-0.376	4.9189	-0.1116	-0.0472	0.6072	0.0203	-0.0416	0.0299	0.0257	-0.2226	0.1396	0.6939	0.132	-0.0821	0.538	-0.0453	0.4951	10.2391	82.6974	104.5981
7	5.7199	0.9677	0.2775	8.7773	2.0325	5.9611	-0.1804	0.0108	-0.6532	0.5514	0.2222	-0.1767	1.6196	0.6966	-0.0291	1.0806	0.1755	0.0246	0.6149	-0.0984	0.5829	-11.1629	76.0119	147.4897
8	2.9339	-0.3994	-2.3268	1.6688	0.2574	4.0946	-0.3738	-0.4486	-0.541	-0.0183	0.082	-0.0351	1.1571	0.8546	0.2105	0.8806	0.26	0.0208	0.6829	0.1014	0.5735	-16.4309	80.2594	178.5826
9	4.9145	-0.6667	1.5705	5.9544	-0.0182	4.1097	-0.2555	-0.6066	1.0778	0.2921	0.1629	-0.2138	-0.3537	-0.0623	0.1279	0.8313	-0.1648	0.1585	0.6531	-0.369	1.2053	7.2334	128.9498	167.3933
10	1.7541	-1.8037	-1.435	7.0823	3.3031	3.579	0.0793	0.0288	0.0598	0.0152	-0.2257	0.2307	-0.0026	-0.0256	0.2084	0.2656	-0.005	0.0004	0.4247	-0.0009	0.4536	27.7122	80.0111	128.4124
11	1.3687	-0.6385	-0.1053	2.8644	0.555	2.4823	0.2764	0.2664	-0.009	-0.6862	-0.2291	-0.1213	0.0242	0.1794	-0.082	0.6008	0.1016	0.14	0.5378	0.0198	0.4627	37.1466	66.6228	108.3931
12	6.3721	-3.0212	-0.6335	4.3711	0.5831	1.5767	-0.0669	0.4295	0.5342	-0.6983	0.2302	-0.1837	-0.1023	0.0477	-0.2284	0.7817	-0.208	0.0897	0.4849	-0.0656	0.6327	-1.3697	117.7724	153.4323
13	1.3144	-0.565	0.0219	5.3507	-0.2848	1.8803	0.0274	-0.1605	-0.1335	0.3759	-0.0265	0.2383	0.1828	-0.1076	0.038	0.37	-0.1055	0.0081	0.4851	0.0148	0.4407	28.0328	54.5697	131.6349

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 113 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 114 through 216 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 217 through 293 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 294 through 373 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 53 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 54 through 134 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 135 through 202 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 203 through 367 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 11 through 113 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 114 through 244 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 245 through 373 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 11 through 134 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 135 through 366 )

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