← Back to search

9u76

;Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K 1.77 angstrom ;

Method: X-RAY DIFFRACTION D_max: 59.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9u76
deposition_date	2025-03-24
last_revision	2026-03-25
title	;Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K 1.77 angstrom ;
keywords	MTAP, complex, phosphorylase, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	18.97 Å
rg_electron	17.87 Å
i0	17238400.00
molecular_weight	30849.0 kDa
excluded_volume	38414 Å³
envelope_volume	43457 Å³
shell_volume	19894 Å³
envelope_diameter	60.4 Å
shell_rg	24.61 Å
envelope_rg	18.20 Å
shape_rg	17.88 Å
total_rg	18.79 Å
total_atoms	2167
n_residues	273
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

▼

3. P(r) Analysis (GNOM)

dmax	59.7 Å
rg_real	18.84 Å
rg_real_error	0.27 Å
i0_real	1.7240e+07
i0_real_error	1.8280e+05
rg_reciprocal	18.86 Å
i0_reciprocal	17240000.0000
total_estimate	0.8921
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.9 Å
skewness	0.140
kurtosis	-0.371
angular_range	— – 0.4200 Å⁻¹
current_alpha	0.0000
highest_alpha	4906000.0000
n_real_points	73
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.997

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	;S-methyl-5'-thioadenosine phosphorylase ;
formula_weight	30777.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2230

MFEITRPPGVRAHVGVIGGSGLYDPGIVENPVEVKVSTPYGNPSDFIVVGDVAGVKVAFLPRHGRGHRIPPHAINYRANIWALKALGVKWVISVSAVGSLREDYRPGDFVVPDQFIDMTKNRRHYTFYDGPVTVHVSMADPFCEDLRQRLIDSGRRLGYTVHERGTYVCIEGPRFSTRAESRVWKDVFKADIIGMTLVPEINLACEAQLCYATLAMVTDYDVWADRPVTAEEVERVMISNVERARRMLYDVIPKLAGEPELERCSCCRALDTAAI

Source

organism	Aeropyrum pernix K1
ncbi_taxonomy_id	272557
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	5'-DEOXY-5'-METHYLTHIOADENOSINE
formula_weight	297.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	45

▶

6. Citations (1)

▶

length_a	79.048 Å
length_b	79.048 Å
length_c	233.480 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	H 3 2
int_tables_number	155
crystal_system	—

resolution	1.770 Å
resolution_low	38.944 Å
r_factor	—
r_work	0.1406
r_free	0.1754

fit	/app/data/saxs_computation/u7/9u76/9u76.fit
pddf	/app/data/pr_computation/u7/9u76/9u76.pr.out
profile	/app/data/saxs_computation/u7/9u76/9u76.dat

;Crystal Structure of 5'-Deoxy-5'-methylthioadenosine phosphorylase from Aeropyrum pernix complex with 5'-Deoxy-5'-methylthioadenosine 353K 1.77 angstrom ;

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