Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo

Method: ELECTRON MICROSCOPY D_max: 115.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uz6
deposition_date	2025-05-16
title	Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo
keywords	(de)carboxylase;PLP-dependent enzymes;dimer, OXIDOREDUCTASE; OXIDOREDUCTASE
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	36.85 Å
rg_electron	35.92 Å
i0	620208000.00
molecular_weight	202010.0 kDa
excluded_volume	252320 Å³
envelope_volume	299860 Å³
shell_volume	66082 Å³
envelope_diameter	125.0 Å
shell_rg	44.69 Å
envelope_rg	35.98 Å
shape_rg	35.93 Å
total_rg	36.38 Å
total_atoms	14192
n_residues	1866
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	115.2 Å
rg_real	36.66 Å
rg_real_error	0.63 Å
i0_real	6.2020e+08
i0_real_error	8.6040e+06
rg_reciprocal	36.78 Å
i0_reciprocal	620300000.0000
total_estimate	0.8948
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.5 Å
skewness	0.188
kurtosis	-0.424
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	145500000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.890

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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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	2.320 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.32 Å
resolution_method	—
num_particles	1975829

description	Glycine dehydrogenase (decarboxylating)
formula_weight	105616.5 kDa
ec_number	1.4.4.2
src_method	man
entity_count	2

Cryo-EM structure of E. coli glycine decarboxylase (P-protein) apo

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Escherichia coli str. K-12 substr. DH10B
ncbi_taxonomy_id	316385
host_organism	Cloning vector pET-28a-ZaTdT12

fit	/app/data/saxs_computation/uz/9uz6/9uz6.fit
pddf	/app/data/pr_computation/uz/9uz6/9uz6.pr.out
profile	/app/data/saxs_computation/uz/9uz6/9uz6.dat

type	polypeptide(L)
strand_id	A,B
atom_count	14192