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9skr

Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, hexamer

Method: ELECTRON MICROSCOPY D_max: 104.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9skr
deposition_date	2025-09-02
title	Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, hexamer
keywords	Carbonic anhydrase, carboxysome, CO2 concentration mechanism, LYASE; LYASE
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	32.56 Å
rg_electron	31.91 Å
i0	176144000.00
molecular_weight	104180.0 kDa
excluded_volume	129600 Å³
envelope_volume	163680 Å³
shell_volume	42808 Å³
envelope_diameter	106.5 Å
shell_rg	38.97 Å
envelope_rg	31.94 Å
shape_rg	31.91 Å
total_rg	32.48 Å
total_atoms	14370
n_residues	934
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	104.6 Å
rg_real	32.52 Å
rg_real_error	0.64 Å
i0_real	1.7610e+08
i0_real_error	2.8050e+06
rg_reciprocal	32.54 Å
i0_reciprocal	176100000.0000
total_estimate	0.8983
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.2 Å
skewness	0.275
kurtosis	-0.564
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	38370000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.942

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Maltose/maltodextrin-binding periplasmic protein,Carboxysome shell carbonic anhydrase
formula_weight	102044.8 kDa
ec_number	4.2.1.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	14731

MWSHPQFEKGSSMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTNSSSNNNNNNNNNNLGIEENLYFQSNANTRNTRSKQRAPFGVSSSVKPRLDLIEQAPNPAYDRHPACITLPERTCRHPLTDLEANEQLGRCEDSVKNRFDRVIPFLQVVAGIPLGLDYVTRVQELAQSSLGHTLPEELLKDNWISGHNLKGIFGYATAKALTAATEQFSRKIMSEKDDSASAIGFFLDCGFHAVDISPCADGRLKGLLPYILRLPLTAFTYRKAYAGSMFDIEDDLAQWEKNELRRYREGVPNTADQPTRYLKIAVYHFSTSDPTHSGCAAHGSNDRAALEAALTQLMKFREAVENAHCCGASIDILLIGVDTDTDAIRVHIPDSKGFLNPYRYVDNTVTYAQTLHLAPDEARVIIHEAILNANRSDGWAKGNGVASEGMRRFIGQLLINNLSQIDYVVNRHGGRYPPNDIGHAERYISVGDGFDEVQIRNLAYYAHLDTVEENAIDVDVGIKIFTKLNLSRGLPIPIAIHYRYDPNVPGSRERTVVKARRIYNAIKERFSSLDEQNLLQFRLSVQAQDIGSPIEEVASA

Source

organism	Halothiobacillus neapolitanus c2
ncbi_taxonomy_id	555778
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	361

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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	2.130 Å
resolution_low	312.000 Å
r_factor	—
r_work	—
r_free	—

resolution	2.13 Å
resolution_method	—
num_particles	486613

fit	/app/data/saxs_computation/sk/9skr/9skr.fit
pddf	/app/data/pr_computation/sk/9skr/9skr.pr.out
profile	/app/data/saxs_computation/sk/9skr/9skr.dat

Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, hexamer

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