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9unz

;Crystal structure of the V165A/S219E/A225P mutant of alanine dehyrogenase from Geobacillus stearothermophilus in complex with nicotinamide cytosine dinucleotide ;

Method: X-RAY DIFFRACTION D_max: 194.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9unz
deposition_date	2025-04-24
title	;Crystal structure of the V165A/S219E/A225P mutant of alanine dehyrogenase from Geobacillus stearothermophilus in complex with nicotinamide cytosine dinucleotide ;
keywords	Non-natural cofactor, amino acid dehydrogenation, OXIDOREDUCTASE; OXIDOREDUCTASE
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	60.13 Å
rg_electron	60.45 Å
i0	6488000000.00
molecular_weight	445260.0 kDa
excluded_volume	428950 Å³
envelope_volume	857520 Å³
shell_volume	121210 Å³
envelope_diameter	213.5 Å
shell_rg	58.96 Å
envelope_rg	60.04 Å
shape_rg	60.45 Å
total_rg	60.43 Å
total_atoms	33684
n_residues	4452
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	194.0 Å
rg_real	60.49 Å
rg_real_error	1.94 Å
i0_real	6.4880e+09
i0_real_error	1.3840e+08
rg_reciprocal	59.80 Å
i0_reciprocal	6481000000.0000
total_estimate	0.8164
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.7 Å
skewness	0.547
kurtosis	-0.155
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	221000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.060

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Alanine dehydrogenase
formula_weight	39451.1 kDa
ec_number	1.4.1.1
mutation	A225P, V165A, S219E
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	34373

MKIGIPKEIKNNENRVAITPAGVMTLVKAGHDVYVETEAGAGSGFSDSEYEKAGAVIVTKAEDAWAAEMVLKVKEPLAEEFRYFRPGLILFTYLHLAAAEALTKALVEQKVVGIAYETVQLANGSLPLLTPMSEVAGRMSVQVGAQFLEKPHGGKGILLGGVPGARRGKVTIIGGGTAGTNAAKIAVGLGADVTILDINAERLRELDDLFGDQVTTLMENSYHIPECVRESDLVVGAVLIPGAKAPKLVTEEMVRSMTPGSVLVDVAIDQGGIFETTDRVTTHDDPTYVKHGVVHYAVANMPGAVPRTSTFALTNVTIPYALQIANKGYRAACLDNPALLKGINTLDGHIVYEAVAAAHNMPYTDVHSLLQG

Source

organism	Geobacillus stearothermophilus
ncbi_taxonomy_id	1422
host_organism	Escherichia coli

Entity 2 non-polymer

description	;[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate ;
formula_weight	640.4 kDa
src_method	syn
entity_count	12

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	689

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6. Citations (1)

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length_a	89.441 Å
length_b	155.752 Å
length_c	178.091 Å
angle_alpha	90.00 °
angle_beta	98.25 °
angle_gamma	90.00 °
z_pdb	24

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.560 Å
resolution_low	46.000 Å
r_factor	0.1958
r_work	0.1932
r_free	0.2443

fit	/app/data/saxs_computation/un/9unz/9unz.fit
pddf	/app/data/pr_computation/un/9unz/9unz.pr.out
profile	/app/data/saxs_computation/un/9unz/9unz.dat

;Crystal structure of the V165A/S219E/A225P mutant of alanine dehyrogenase from Geobacillus stearothermophilus in complex with nicotinamide cytosine dinucleotide ;

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