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9r22

Cryo-EM structure of the light-driven proton pump PsPR in detergent micelle

Method: ELECTRON MICROSCOPY D_max: 91.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r22
deposition_date	2025-04-29
title	Cryo-EM structure of the light-driven proton pump PsPR in detergent micelle
keywords	proton transport, retinal, bioenergetics, proteorhodopsin, microbial rhodopsin, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	31.66 Å
rg_electron	30.12 Å
i0	185748000.00
molecular_weight	134380.0 kDa
excluded_volume	178820 Å³
envelope_volume	194210 Å³
shell_volume	50595 Å³
envelope_diameter	91.8 Å
shell_rg	39.49 Å
envelope_rg	30.06 Å
shape_rg	30.11 Å
total_rg	31.08 Å
total_atoms	9503
n_residues	1150
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	91.8 Å
rg_real	31.38 Å
rg_real_error	0.49 Å
i0_real	1.8570e+08
i0_real_error	2.8410e+06
rg_reciprocal	31.51 Å
i0_reciprocal	185800000.0000
total_estimate	0.9031
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	42.2 Å
skewness	0.034
kurtosis	-0.509
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	24420000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.919

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	microbial rhodopsin
formula_weight	26467.1 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	9643

MLQAGDFVGVSFWLVSVAMVAATVFFFYEGMSVKKEWKLSMTIAGLVTLVAAIHYYYMRDYWVASVLAGSPDSPIVYRYIDWLITVPLLMIEFFIILKAVGASISTNSFWRLLVGTLVMLIGGFAGEAMLISASLGFIIGMVGWAIIIWEIFGGEASKAADANAGVKSAFNALRLIVLVGWAIYPLGYIFGYMMGSVDSGSLNIIYNLADFVNKILFGLIIWNVAVRESSDALEHHHHHH

Source

organism	Candidatus Pseudothioglobus sp.
ncbi_taxonomy_id	3072909
host_organism	Escherichia coli

Entity 2 non-polymer

description	EICOSANE
formula_weight	282.5 kDa
src_method	syn
entity_count	30

Entity 3 non-polymer

description	RETINAL
formula_weight	284.4 kDa
src_method	man
entity_count	5

Source

organism	Candidatus Pseudothioglobus sp.
ncbi_taxonomy_id	3072909
host_organism	Escherichia coli

Entity 4 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	5

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	105

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.480 Å
resolution_low	105.340 Å
r_factor	0.3787
r_work	0.3787
r_free	—

resolution	2.48 Å
resolution_method	—
num_particles	497291

fit	/app/data/saxs_computation/r2/9r22/9r22.fit
pddf	/app/data/pr_computation/r2/9r22/9r22.pr.out
profile	/app/data/saxs_computation/r2/9r22/9r22.dat

Cryo-EM structure of the light-driven proton pump PsPR in detergent micelle

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 non-polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)