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9vae

Crystal structure of alanine dehydrogenase-like protein from Thermus thermophilus

Method: X-RAY DIFFRACTION D_max: 71.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vae
deposition_date	2025-06-03
last_revision	2026-06-10
title	Crystal structure of alanine dehydrogenase-like protein from Thermus thermophilus
keywords	alanine dehydrogenase-like protein, NAD(H)-binding protein, SIGNALING PROTEIN; SIGNALING PROTEIN
method	X-RAY DIFFRACTION

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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	22.33 Å
rg_electron	21.48 Å
i0	22187900.00
molecular_weight	36176.0 kDa
excluded_volume	45499 Å³
envelope_volume	53294 Å³
shell_volume	21066 Å³
envelope_diameter	73.7 Å
shell_rg	27.58 Å
envelope_rg	21.62 Å
shape_rg	21.49 Å
total_rg	22.25 Å
total_atoms	2544
n_residues	338
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	71.0 Å
rg_real	22.33 Å
rg_real_error	0.44 Å
i0_real	2.2190e+07
i0_real_error	2.9920e+05
rg_reciprocal	22.33 Å
i0_reciprocal	22190000.0000
total_estimate	0.8970
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.7 Å
skewness	0.333
kurtosis	-0.494
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	6232000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	alanine dehydrogenase
formula_weight	36441.1 kDa
ec_number	1.4.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2610

MEFGVPKERSGGEIPERRVPLTPQGVRELVASGHRVYVERGAGEGAGFPDEAYEEAGARLVGREEAFGRPQVVLKVARPTLEEVGLMRKNAVLMAFLHLAVAESPLVEAMAQKGLTAIGYELVGEEGRRPVLKAMSEIAGRMAPQLAGRLLEAPQGPGILLSGLVGIPPADVVVLGAGVLGRAAARAFLGAGASVHLLDRALPPLEEAAREAPGAITALVTQDRLERYVAFADVLVGAVAVPGERTPLLLTRGLLARMRPGSVLLDFSIDQGGVSETSRPGVYQEMGVTHFCLPNVPALVPRTASHALTATLLPYLLRIQEDPLALPGLRQGAYLLFGEKGGHLE

Source

organism	Thermus thermophilus HB27
ncbi_taxonomy_id	262724
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	66

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6. Citations (1)

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length_a	86.060 Å
length_b	86.060 Å
length_c	178.203 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63 2 2
int_tables_number	182
crystal_system	—

resolution	2.500 Å
resolution_low	46.500 Å
r_factor	0.2281
r_work	0.2252
r_free	0.2858

fit	/app/data/saxs_computation/va/9vae/9vae.fit
pddf	/app/data/pr_computation/va/9vae/9vae.pr.out
profile	/app/data/saxs_computation/va/9vae/9vae.dat

Crystal structure of alanine dehydrogenase-like protein from Thermus thermophilus

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

Diffraction