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9t09

X-ray structure of the catalytic domain of CDC25B C473S at 1.34 angstrom resolution

Method: X-RAY DIFFRACTION D_max: 57.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t09
deposition_date	2025-10-16
title	X-ray structure of the catalytic domain of CDC25B C473S at 1.34 angstrom resolution
keywords	CDC25B, Catalytic Domain, Phosphatase, Cell Division Cycle 25B, HYDROLASE; HYDROLASE
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	17.49 Å
rg_electron	16.32 Å
i0	9061390.00
molecular_weight	21837.0 kDa
excluded_volume	27135 Å³
envelope_volume	31068 Å³
shell_volume	15901 Å³
envelope_diameter	56.6 Å
shell_rg	22.50 Å
envelope_rg	16.72 Å
shape_rg	16.31 Å
total_rg	17.36 Å
total_atoms	1526
n_residues	180
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	57.8 Å
rg_real	17.39 Å
rg_real_error	0.36 Å
i0_real	9.0610e+06
i0_real_error	1.1460e+05
rg_reciprocal	17.40 Å
i0_reciprocal	9061000.0000
total_estimate	0.8810
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.1 Å
skewness	0.180
kurtosis	-0.351
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0000
highest_alpha	2042000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	M-phase inducer phosphatase 2
formula_weight	22995.3 kDa
ec_number	3.1.3.48
mutation	C473S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1939

MGSSHHHHHHSSGLVPRGSHMASELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPCSLDKRVILIFHSEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSW

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	270

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6. Citations (1)

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length_a	52.130 Å
length_b	71.200 Å
length_c	72.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.340 Å
resolution_low	42.400 Å
r_factor	0.1582
r_work	0.1573
r_free	0.1754

fit	/app/data/saxs_computation/t0/9t09/9t09.fit
pddf	/app/data/pr_computation/t0/9t09/9t09.pr.out
profile	/app/data/saxs_computation/t0/9t09/9t09.dat