PDB-3qap: Crystal structure of Natronomonas pharaonis sensory rhodopsin II ...

ID or keywords:

Entry

Database: PDB / ID: 3qap

Title

Crystal structure of Natronomonas pharaonis sensory rhodopsin II in the ground state

Components

Sensory rhodopsin-2

Keywords

TRANSPORT PROTEIN /

Phototaxis / NpHtrII /

Membrane

Function / homology

Function and homology information

photoreceptor activity /

phototransduction / monoatomic ion channel activity /

plasma membrane
Similarity search - Function

Biological species

Natronomonas pharaonis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Gushchin, I. / Reshetnyak, A. / Borshchevskiy, V. / Ishchenko, A. / Round, E. / Grudinin, S. / Engelhard, M. / Buldt, G. / Gordeliy, V.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Active State of Sensory Rhodopsin II: Structural Determinants for Signal Transfer and Proton Pumping.
Authors: Gushchin, I. / Reshetnyak, A. / Borshchevskiy, V. / Ishchenko, A. / Round, E. / Grudinin, S. / Engelhard, M. / Buldt, G. / Gordeliy, V.

History

Deposition	Jan 11, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 14, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2011	Group: Database references
Revision 1.2	Jul 29, 2020	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3	Feb 21, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3qap.cif.gz	113.4 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qa/3qap ftp://data.pdbj.org/pub/pdb/validation_reports/qa/3qap	HTTPS FTP

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Related structure data

Related structure data	3qdcC C: citing same article (ref.)
Similar structure data	3wd6-1 3wd6-3 3wd6-4 3omq-1 6uav-d 5ueh-d 3wd6-2 5yvn-d 6pnm-d 4pqi-d 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	#27 - Mar 2002 Bacteriorhodopsin similarity (9) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (7) #144 - Dec 2011 Complex I similarity (1) #147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #58 - Oct 2004 G Proteins similarity (1) #66 - Jun 2005 Carotenoid Oxygenase similarity (1)

Deposited unit

A: Sensory rhodopsin-2

hetero molecules

35.4 kDa, 1 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)	86.990, 128.090, 50.630
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein

Sensory rhodopsin-2 / Sensory rhodopsin II / SR-II

Mass: 25368.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Natronomonas pharaonis (archaea) / Gene: sop2, sopII / Production host:

Escherichia coli (E. coli) / References: UniProt: P42196

#3: Sugar

ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside /

Octyl glucoside

Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₁₄H₂₈O₆ / Comment: detergent*YM

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Non-polymers , 4 types, 105 molecules

#2: Chemical	ChemComp-RET / RETINAL / Retinal Mass: 284.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₀H₂₈O
#4: Chemical	... ChemComp-LFA / EICOSANE / LIPID FRAGMENT / Icosane Mass: 282.547 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C₂₀H₄₂
#5: Chemical	ChemComp-L2P / 2,3-DI-PHYTANYL-GLYCEROL / 1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL Mass: 653.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₃H₈₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.78 Å³/Da / Density % sol: 55.75 %
Crystal grow	Temperature: 295.5 K / Method: lipidic cubic phase / pH: 5.1 Details: 1M Na/KPi, 0.3M trehalose, pH 5.1, Lipidic cubic phase, temperature 295.5K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.934 Å / Relative weight: 1
Reflection	Resolution: 1.9→22.11 Å / Num. all: 21333 / Num. obs: 20672 / % possible obs: 96.9 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2
Reflection shell	Resolution: 1.9→2 Å / % possible all: 97.4

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→22 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.958 / SU B: 4.589 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17306	1107	5.1 %	RANDOM
R_work	0.15236	-	-	-
obs	0.15343	20672	95.91 %	-
all	-	21333	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 30.479 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.61 Å²	0 Å²	0 Å²
2-	-	-0.17 Å²	0 Å²
3-	-	-	-0.44 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1633	0	375	73	2081

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.023	2090
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.248	2.081	2750
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.049	5	240
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.41	20.2	50
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.94	15	258
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.041	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	319
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	1299
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.628	1.5	1113
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.997	2	1798
X-RAY DIFFRACTION	r_scbond_it	1.331	3	977
X-RAY DIFFRACTION	r_scangle_it	1.974	4.5	942
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.246	103	-
R_work	0.201	1464	-
obs	-	-	95.84 %

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	6.8731	4.1925	-0.5368	6.4697	1.4686	6.6613	-0.1885	0.0443	0.5141	-0.1677	0.2129	0.3757	-0.4246	-0.2688	-0.0244	0.0573	0.039	-0.044	0.174	0.0033	0.0842	3.946	40.082	-6.922
2	3.1178	1.6088	0.6199	9.0898	-3.7169	4.5816	0.1224	-0.1766	-0.2836	-0.3665	0.119	0.5617	0.493	-0.4731	-0.2415	0.061	-0.0854	-0.0285	0.2183	0.0075	0.121	-0.462	19.419	-3.149
3	2.0395	-1.6566	0.6347	8.9014	-1.0128	2.4648	0.0811	0.0016	-0.1148	0.1351	-0.0629	0.4426	0.1674	-0.3966	-0.0181	0.0202	-0.021	0.0091	0.2079	-0.0046	0.0284	2.616	26.764	1.116
4	6.2126	4.4237	3.7615	3.5241	4.1825	8.7658	0.0221	-0.1979	0.4368	-0.007	-0.2026	0.26	-0.3619	-0.2597	0.1806	0.3816	0.0981	-0.1509	0.1775	0.0098	0.3409	8.499	47.326	4.985
5	7.3298	-1.442	6.8083	0.8355	-0.7362	6.9996	-0.3394	0.0853	0.4314	-0.0739	-0.1108	-0.0223	-0.4485	0.0103	0.4502	0.1539	0.031	-0.0069	0.2097	-0.0293	0.0995	10.318	40.603	4.706
6	0.8975	-1.6091	0.1104	9.78	1.0095	2.262	0.015	-0.1807	-0.07	0.291	0.0206	0.1632	0.3286	-0.2358	-0.0357	0.0815	-0.0333	-0.0007	0.1089	0.0161	0.0273	10.742	21.806	6.157
7	3.681	3.1523	1.3372	10.3004	10.9683	13.1848	0.1868	-0.2831	-0.3264	0.9979	-0.2875	-0.1069	1.1901	-0.155	0.1008	0.5197	0.0298	-0.0231	0.0756	-0.0174	0.0653	17.382	12.448	14.485
8	1.0037	0.841	0.232	4.865	0.0241	1.8886	0.0066	0.0001	0.0636	0.2078	-0.0588	0.1465	-0.1196	0.0218	0.0523	0.0909	0.0294	-0.0007	0.1185	-0.0004	0.0072	19.285	35.316	12.513
9	0.0864	0.6726	0.3406	7.6254	2.8551	2.2274	0.073	0.0124	-0.0344	0.0662	-0.0369	-0.198	0.2787	0.2104	-0.0362	0.1672	0.0502	-0.0384	0.1574	-0.0125	0.0795	24.249	20.993	7.705
10	10.4021	1.5907	1.3204	17.9186	-2.816	16.5429	-0.0112	0.0314	-0.0936	0.0052	-0.0466	-0.0563	0.4465	0.1977	0.0579	0.2249	0.0255	0.0002	0.0312	-0.0511	0.1001	17.337	4.459	0.064
11	0.7797	1.0038	0.3333	7.5638	0.663	1.8896	0.092	0.0843	-0.0353	-0.2232	-0.0945	-0.0381	0.3124	0.1233	0.0025	0.1138	0.0457	-0.0095	0.1428	-0.0151	0.0363	19.22	21.155	-2.213
12	1.6839	-0.0226	-1.0018	3.6428	-0.0733	0.9553	0.0443	0.021	0.0396	0.1214	-0.1033	-0.1483	-0.1994	0.1904	0.059	0.1807	-0.023	-0.0266	0.2058	0.0211	0.0792	21	42.619	-0.543
13	1.1359	0.7173	0.9431	3.6939	0.7717	2.6782	0.0973	0.0629	0.0186	-0.1366	-0.0881	0.1594	0.138	-0.0595	-0.0091	0.0277	0.0141	-0.0023	0.1238	-0.0083	0.0172	11.756	28.953	-5.996
14	8.5085	-7.2591	-0.5897	48.0854	8.0047	9.8817	0.3968	0.5244	-1.4646	-0.4106	-0.0308	0.7233	1.3325	-0.3011	-0.3661	0.5729	0.0163	-0.2471	0.2254	-0.1358	0.3411	7.382	9.541	-8.873

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 12
2	X-RAY DIFFRACTION	2	A	13 - 35
3	X-RAY DIFFRACTION	3	A	36 - 55
4	X-RAY DIFFRACTION	4	A	56 - 66
5	X-RAY DIFFRACTION	5	A	67 - 73
6	X-RAY DIFFRACTION	6	A	74 - 92
7	X-RAY DIFFRACTION	7	A	93 - 98
8	X-RAY DIFFRACTION	8	A	99 - 126
9	X-RAY DIFFRACTION	9	A	127 - 149
10	X-RAY DIFFRACTION	10	A	150 - 157
11	X-RAY DIFFRACTION	11	A	158 - 175
12	X-RAY DIFFRACTION	12	A	176 - 191
13	X-RAY DIFFRACTION	13	A	192 - 212
14	X-RAY DIFFRACTION	14	A	213 - 219

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