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9skt

Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, dimer, minor state

Method: ELECTRON MICROSCOPY D_max: 105.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9skt
deposition_date	2025-09-02
title	Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, dimer, minor state
keywords	Carbonic anhydrase, carboxysome, CO2 concentration mechanism, LYASE, Structural Genomics; 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	33.00 Å
rg_electron	32.41 Å
i0	179006000.00
molecular_weight	105060.0 kDa
excluded_volume	130710 Å³
envelope_volume	165930 Å³
shell_volume	42993 Å³
envelope_diameter	111.3 Å
shell_rg	39.13 Å
envelope_rg	32.29 Å
shape_rg	32.40 Å
total_rg	32.96 Å
total_atoms	14494
n_residues	942
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	105.1 Å
rg_real	32.96 Å
rg_real_error	0.74 Å
i0_real	1.7900e+08
i0_real_error	2.7310e+06
rg_reciprocal	32.98 Å
i0_reciprocal	179000000.0000
total_estimate	0.8993
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	35.0 Å
skewness	0.278
kurtosis	-0.554
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	37590000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.913

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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	14641

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	147

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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	2.450 Å
resolution_low	312.000 Å
r_factor	—
r_work	—
r_free	—

resolution	2.45 Å
resolution_method	—
num_particles	277721

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

Cryo-EM structure of H. neapolitanus CsoSCA in oxidizing conditions, dimer, minor state

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