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9s7j

Cryo-EM (200kV) structure of pyruvate decarboxylase from Neoasaia chiangmaiensis

Method: ELECTRON MICROSCOPY D_max: 115.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s7j
deposition_date	2025-08-04
title	Cryo-EM (200kV) structure of pyruvate decarboxylase from Neoasaia chiangmaiensis
keywords	metabolic enzyme pyruvate decarboxylase CO2 fixation, CYTOSOLIC PROTEIN; CYTOSOLIC 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	37.57 Å
rg_electron	36.61 Å
i0	897449000.00
molecular_weight	239540.0 kDa
excluded_volume	297210 Å³
envelope_volume	341280 Å³
shell_volume	72980 Å³
envelope_diameter	125.1 Å
shell_rg	45.86 Å
envelope_rg	36.62 Å
shape_rg	36.59 Å
total_rg	37.17 Å
total_atoms	16816
n_residues	2212
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	115.4 Å
rg_real	37.31 Å
rg_real_error	0.70 Å
i0_real	8.9740e+08
i0_real_error	1.4300e+07
rg_reciprocal	37.47 Å
i0_reciprocal	897600000.0000
total_estimate	0.8982
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.7 Å
skewness	0.119
kurtosis	-0.543
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	288100000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.911

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	pyruvate decarboxylase
formula_weight	62184.2 kDa
ec_number	4.1.1.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16816

MGSSHHHHHHSSGLVPRGSHMAYTVGMYLAERLAQIGLKHHFAVAGDYNLVLLDQLLLNKDMEQIYCCNELNCGFSAEGYARAQGAAAAVVTFSVGAISAMNAIGGAYAENLPVILISGAPNSNDHGSGHVLHHTIGTTDYGYQLEMVRHLTCAAESIVSAENAPAKIDHVIRTALRERKPAYLEIACNVAGAECVRPGPVSSLLPETPSDLTSLQAALDASLAWLAPRDRVVLLVGSKLRAADAQAVSVELADRMGCAVTIMAAAKGFFPEDHPCYRGLYWGEVSSPGVQELVESADGIICLAPVFNDYSTVGWNAWPKGDNVLLAEPDRVTVAGRSYEGIALRDFIKGMTARALSKPVTAQGTTAPRLELAQAKGDAPLTNDEMTRQIQALLNRDTTLTAETGDSWFNATRMNLPGGARVELEMQWGHIGWSVPSAFGNAMGSQDRRHVLMVGDGSFQLTAQEVAQMIRYELPVIIFLVNNRGYVIEIAIHDGPYNYIKNWDYAGLIAAFNAGEGHGLGLHAKTGDELQDAIEKAVANKRGPTLIECSIARDDCTSELVNWGKRVAATNSRRPAAD

Source

organism	Neoasaia chiangmaiensis
ncbi_taxonomy_id	320497
host_organism	Escherichia coli

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	THIAMINE DIPHOSPHATE
formula_weight	425.3 kDa
src_method	syn
entity_count	4

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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	triclinic

resolution	2.85 Å
resolution_method	—
num_particles	314682

fit	/app/data/saxs_computation/s7/9s7j/9s7j.fit
pddf	/app/data/pr_computation/s7/9s7j/9s7j.pr.out
profile	/app/data/saxs_computation/s7/9s7j/9s7j.dat