Cryo-EM structure of IDH1 R132H

Method: ELECTRON MICROSCOPY D_max: 90.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yha
deposition_date	2025-09-30
title	Cryo-EM structure of IDH1 R132H
keywords	Dehydrogenase, cellular metabolism, oxidative decarboxylation, 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	29.77 Å
rg_electron	28.91 Å
i0	134616000.00
molecular_weight	91212.0 kDa
excluded_volume	114160 Å³
envelope_volume	146250 Å³
shell_volume	41652 Å³
envelope_diameter	94.8 Å
shell_rg	36.81 Å
envelope_rg	28.38 Å
shape_rg	28.92 Å
total_rg	29.63 Å
total_atoms	6408
n_residues	794
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	90.0 Å
rg_real	29.60 Å
rg_real_error	0.47 Å
i0_real	1.3460e+08
i0_real_error	1.9540e+06
rg_reciprocal	29.67 Å
i0_reciprocal	134600000.0000
total_estimate	0.9078
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	39.1 Å
skewness	0.113
kurtosis	-0.533
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	27390000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.952

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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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	2.69 Å
resolution_method	—
num_particles	103976

description	Isocitrate dehydrogenase [NADP] cytoplasmic
formula_weight	47859.4 kDa
ec_number	1.1.1.42
mutation	R132H
src_method	man
entity_count	2

type	polypeptide(L)
strand_id	A,B
atom_count	6408

Cryo-EM structure of IDH1 R132H

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	743.4 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/yh/9yha/9yha.fit
pddf	/app/data/pr_computation/yh/9yha/9yha.pr.out
profile	/app/data/saxs_computation/yh/9yha/9yha.dat