PDB-5azd: Crystal structure of thermophilic rhodopsin.

ID or keywords:

Entry

Database: PDB / ID: 5azd

Title

Crystal structure of thermophilic rhodopsin.

Components

Bacteriorhodopsin

Keywords

TRANSPORT PROTEIN / Membrane protein / Retinal / Ion pump / Thermal stability

Function / homology

Function and homology information

monoatomic ion channel activity / photoreceptor activity / phototransduction / membrane
Similarity search - Function

Biological species

Thermus thermophilus JL-18 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Mizutani, K. / Hashimoto, N. / Tsukamoto, T. / Yamashita, K. / Yamamoto, M. / Sudo, Y. / Murata, T.

Funding support

Japan, 1items

Citation

Journal: To Be Published
Title: X-ray crystallographic structure of thermophilic rhodopsin: implications for high thermal stability and optogenetic availability.
Authors: Tsukamoto, T. / Mizutani, K. / Hasegawa, T. / Takahashi, M. / Hashimoto, N. / Shimono, K. / Yamashita, K. / Yamamoto, M. / Miyauchi, S. / Takagi, S. / Hayashi, S. / Sudo, Y. / Murata, T.

History

Deposition	Sep 30, 2015	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 27, 2016	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2020	Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Nov 8, 2023	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	5azd.cif.gz	398.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5azd.ent.gz	331.5 KB	Display	PDB format
PDBx/mmJSON format	5azd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5azd_validation.pdf.gz	468.9 KB	Display	wwPDB validaton report
Full document	5azd_full_validation.pdf.gz	482.7 KB	Display
Data in XML	5azd_validation.xml.gz	35.6 KB	Display
Data in CIF	5azd_validation.cif.gz	47 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/az/5azd ftp://data.pdbj.org/pub/pdb/validation_reports/az/5azd	HTTPS FTP

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Related structure data

Related structure data	3ddlS S: Starting model for refinement
Similar structure data	5b2n-d 2rin-1 5ztk-d 5ztl-d 6jy6-d 2rf1-2 2reg-2 7crj-d 5fjg-d 5jrf-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) 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

3ddlS

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	#27 - Mar 2002 Bacteriorhodopsin similarity (5) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (5)

Deposited unit

A: Bacteriorhodopsin

B: Bacteriorhodopsin

C: Bacteriorhodopsin

D: Bacteriorhodopsin

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

1

A: Bacteriorhodopsin

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

2

B: Bacteriorhodopsin

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

3

C: Bacteriorhodopsin

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

4

D: Bacteriorhodopsin

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

5

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	63.186, 67.693, 73.045
Angle α, β, γ (deg.)	116.48, 114.14, 90.82
Int Tables number	1
Space group name H-M	P1

#1: Protein	Bacteriorhodopsin / thermophilic rhodopsin Mass: 30307.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_1346 / Plasmid: pKI81 / Details (production host): pBAD derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9ZSC3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Bacteriorhodopsin / thermophilic rhodopsin

Mass: 30307.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus thermophilus JL-18 (bacteria) / Gene: TtJL18_1346 / Plasmid: pKI81 / Details (production host): pBAD derivative / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H9ZSC3

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.28 %
Crystal grow	Temperature: 296 K / Method: lipidic cubic phase / pH: 3.6 / Details: 100mM sodium citrate pH3.6, 34% PEG 400 (v/v)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
Detector	Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 30, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.1 Å / Relative weight: 1
Reflection	Resolution: 2.8→46.52 Å / Num. all: 22129 / Num. obs: 22122 / % possible obs: 93.19 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / B_iso Wilson estimate: 37.5 Å² / R_merge(I) obs: 0.1192 / Net I/σ(I): 6.26
Reflection shell	Resolution: 2.796→2.896 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.4538 / Mean I/σ(I) obs: 1.77 / % possible all: 89.08

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
Coot		model building
PHASER		phasing
XDS		data processing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3DDL

3ddl

Resolution: 2.8→46.519 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 29.54 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2777	1123	5.1 %	Random selection
R_work	0.2284	-	-	-
obs	0.2311	22039	93.31 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→46.519 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7898	0	0	2	7900

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8134
X-RAY DIFFRACTION	f_angle_d	0.737	11139
X-RAY DIFFRACTION	f_dihedral_angle_d	16.765	4788
X-RAY DIFFRACTION	f_chiral_restr	0.032	1281
X-RAY DIFFRACTION	f_plane_restr	0.004	1337

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 (%)
2.8002-2.9276	0.3056	138	0.2784	2615	X-RAY DIFFRACTION	94
2.9276-3.0819	0.3478	144	0.2789	2699	X-RAY DIFFRACTION	96
3.0819-3.275	0.3059	116	0.2563	2739	X-RAY DIFFRACTION	96
3.275-3.5277	0.3097	151	0.245	2726	X-RAY DIFFRACTION	97
3.5277-3.8826	0.2773	160	0.222	2671	X-RAY DIFFRACTION	97
3.8826-4.444	0.261	138	0.2068	2579	X-RAY DIFFRACTION	95
4.444-5.5975	0.2769	127	0.2068	2231	X-RAY DIFFRACTION	96
5.5975-46.5254	0.2165	149	0.2009	2656	X-RAY DIFFRACTION	95

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	1.6097	-0.9497	0.4498	3.6429	0.0776	0.6379	-0.1346	-0.102	0.0644	0.5751	0.2755	-0.1893	0.2815	0.1858	-0.1796	0.3331	0.0697	0.0065	0.3164	0.0215	0.1387	17.3065	-69.082	26.4154
2	2.3432	1.8189	1.7585	3.6419	-0.2035	3.6825	0.0823	-0.8785	-0.327	0.2101	0.3416	-0.7155	-0.3296	0.8565	-0.7787	0.5231	-0.0529	-0.0602	0.3776	-0.1755	0.4546	15.9685	-50.5628	35.0529
3	2.4649	1.735	1.4664	2.9883	0.0889	1.4399	-0.3106	0.4504	0.0263	0.2269	0.2614	-0.2661	0.1103	0.423	0.144	0.2882	0.115	-0.0229	0.4012	-0.105	0.3523	33.0501	-70.8031	13.8785
4	0.3709	0.0025	0.3687	1.4637	0.214	0.7979	-0.0483	0.1155	0.0399	0.0195	-0.0069	-0.0953	0.131	-0.0297	0.0097	0.2799	-0.0217	0.0702	0.2963	-0.0783	0.2895	24.3111	-66.785	9.7893
5	0.3942	-0.9642	0.2806	3.3173	0.8541	2.0166	-0.1533	-0.0813	-0.035	0.5672	0.2525	0.0262	0.1341	0.2153	-0.086	0.2184	-0.0173	0.0777	0.2931	-0.0278	0.2597	48.1048	-66.6138	26.567
6	2.9976	-0.3725	1.65	4.0889	-1.5041	2.1474	-0.201	0.4016	-0.1004	0.7998	0.0474	-1.0532	0.0778	0.9276	0.208	0.459	-0.2318	0.1207	0.6047	-0.2076	0.7628	54.5617	-53.1947	32.1228
7	4.9257	-0.6435	-1.2212	0.908	-1.2151	3.0217	-0.0805	-0.189	-0.0421	-0.3224	-0.212	-0.1276	-0.3645	0.6427	0.0112	0.2722	0.0681	0.05	0.3934	-0.0183	0.219	60.8098	-72.3496	13.1236
8	2.1865	0.106	0.451	1.8545	-1.0912	0.7499	-0.0425	0.1242	-0.0548	-0.2785	-0.0432	-0.3089	0.1022	0.3621	0.0823	0.3055	0.0113	0.0746	0.4872	0.0896	0.2598	63.6724	-64.5924	5.6891
9	1.1784	-0.7911	0.4489	1.3719	-1.4337	1.9627	0.0004	0.1436	0.0561	0.0068	0.031	-0.0421	0.3743	0.0623	-0.0306	0.2777	-0.0735	-0.0202	0.2467	-0.0436	0.2729	50.1834	-67.0353	11.1068
10	1.0479	1.4728	1.3418	3.6938	1.5031	3.1488	-0.1694	0.0426	0.0596	-0.4264	0.1093	0.3995	-0.6519	0.1484	0.1039	0.2927	0.004	0.055	0.2196	-0.015	0.2999	8.9963	-73.5344	37.6513
11	0.109	0.2199	0.4651	0.4617	0.7338	4.5567	-0.4743	0.1906	-0.3094	0.2534	-0.0414	0.7341	-0.1723	-0.1747	0.1153	0.6056	-0.013	0.3378	0.4706	-0.131	0.6864	2.8221	-61.957	46.718
12	1.3152	0.1132	-0.6167	0.7723	0.3594	4.1794	-0.1544	-0.0755	-0.1637	0.1293	0.3722	-0.3025	0.4607	-0.856	-0.1657	0.3005	-0.0298	-0.0108	0.428	0.0567	0.3782	-5.8152	-89.2232	47.7471
13	1.1255	0.1957	0.4422	1.2897	-0.7972	2.2101	-0.037	-0.0746	-0.1265	-0.203	0.1346	0.0288	0.1684	0.073	0.0095	0.2746	0.0029	0.0387	0.2701	0.0341	0.3487	7.0249	-87.298	44.7027
14	0.496	0.5366	0.4967	2.722	1.451	1.7573	-0.2621	0.0258	0.1073	-0.2792	0.1545	0.6556	0.0151	0.0569	0.0883	0.3104	-0.0557	-0.0802	0.2455	0.0932	0.3205	40.58	-73.2905	36.7331
15	0.0817	0.0875	0.6534	0.0933	0.6998	5.2289	0.0965	0.0315	-0.2186	0.3963	-0.0798	0.7967	0.0165	-1.5606	0.3282	0.2635	-0.0076	0.1321	0.6282	0.1376	0.7994	35.1427	-59.8743	46.3313
16	1.4567	-1.3971	-2.1246	2.2762	1.5312	3.1855	-0.2349	-0.2496	-0.1239	-0.2594	0.0839	0.56	-0.2309	0.0336	0.1077	0.2027	-0.0464	-0.0993	0.3202	0.0088	0.4552	23.8867	-85.216	45.8533
17	0.8135	-1.2057	-0.7375	2.5941	1.5883	1.8692	0.2452	-0.0238	-0.5202	0.1914	-0.1042	0.0379	0.4372	0.141	0.1087	0.7535	-0.1153	-0.0227	0.1516	-0.15	0.4384	26.8448	-105.3465	41.3128
18	0.6689	-0.3019	0.0344	0.1242	-0.0483	0.8952	-0.0686	-0.0547	-0.0092	-0.1727	0.2285	-0.0074	0.1385	0.2066	-0.128	0.28	-0.0184	0.0417	0.2355	0.0626	0.2805	37.3956	-86.3378	44.0843

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 76 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 77 through 89 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 140 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 141 through 253 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 82 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 83 through 91 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 92 through 114 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 115 through 180 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 181 through 252 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 4 through 82 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 83 through 91 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 92 through 179 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 180 through 254 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 4 through 82 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 83 through 89 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 90 through 167 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 168 through 180 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 181 through 253 )

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