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9tzh

X-ray structure of S. cerevisiae threonlycarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP at 3.7 A resolution

Method: X-RAY DIFFRACTION D_max: 155.0 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tzh
deposition_date	2026-01-22
title	X-ray structure of S. cerevisiae threonlycarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP at 3.7 A resolution
keywords	threonlycarbamoyladenosine dehydratase, t6A, ct6A, modification, tRNA, RNA BINDING PROTEIN; RNA BINDING 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	44.58 Å
rg_electron	44.99 Å
i0	412383000.00
molecular_weight	166750.0 kDa
excluded_volume	209060 Å³
envelope_volume	286200 Å³
shell_volume	55655 Å³
envelope_diameter	164.3 Å
shell_rg	45.52 Å
envelope_rg	45.84 Å
shape_rg	45.02 Å
total_rg	44.91 Å
total_atoms	11689
n_residues	1451
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	155.0 Å
rg_real	44.89 Å
rg_real_error	2.14 Å
i0_real	4.1240e+08
i0_real_error	9.7530e+06
rg_reciprocal	44.58 Å
i0_reciprocal	412200000.0000
total_estimate	0.6131
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	53.1 Å
skewness	0.495
kurtosis	-0.209
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	42230000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.823; Smooth: 0.517

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	tRNA threonylcarbamoyladenosine dehydratase 1
formula_weight	43527.9 kDa
ec_number	6.1.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11689

GSDHLFREQLARNYAFLGEEGMRKIKEQYIVIVGAGEVGSWVCTMLIRSGCQKIMIIDPENISIDSLNTHCCAVLSDIGKPKVQCLKEHLSKIAPWSEIKARAKAWTKENSHDLIFADGESPTFIVDCLDNLESKVDLLEYAHHNKIDVISSMGVATKSDPTRVSINDISMTEFDPISRCVRRKLRKRGIATGISVVFSNEMLDPRRDDILSPIDCEHRAINAVRDEALRHLPELGTMPGIFGLSIATWILTKVSGYPMKENEVKNRLKFYDSILETFQKQMARLNENKERSSLLGLEEVGYIVEEMFRGKSPISGYSTKLALTKWEANKEISLTNVVLMTKEEQEIHEKRILLDGEKLTAVYSEEVLDFIERLFKEEEYYS

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	259.440 Å
length_b	259.440 Å
length_c	236.110 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	48

space_group	P 65 2 2
int_tables_number	179
crystal_system	—

resolution	3.700 Å
resolution_low	49.030 Å
r_factor	0.2732
r_work	0.2726
r_free	0.2847

fit	/app/data/saxs_computation/tz/9tzh/9tzh.fit
pddf	/app/data/pr_computation/tz/9tzh/9tzh.pr.out
profile	/app/data/saxs_computation/tz/9tzh/9tzh.dat

X-ray structure of S. cerevisiae threonlycarbamoyladenosine dehydratase 1 (residues 50-429) in complex with AMP at 3.7 A resolution

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