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9t0a

X-ray structure of the complex between the catalytic domain of CDC25B C473S and 3-O-methylfluorescein phosphate (3-OMFP)

Method: X-RAY DIFFRACTION D_max: 58.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t0a
deposition_date	2025-10-16
title	X-ray structure of the complex between the catalytic domain of CDC25B C473S and 3-O-methylfluorescein phosphate (3-OMFP)
keywords	CDC25B, Catalytic Domain, Phosphatase, Cell Division Cycle 25B, substrate, 3-O-methylfluorescein phosphate, 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	16.55 Å
i0	16307100.00
molecular_weight	20576.0 kDa
excluded_volume	19973 Å³
envelope_volume	31363 Å³
shell_volume	15932 Å³
envelope_diameter	58.7 Å
shell_rg	22.54 Å
envelope_rg	16.95 Å
shape_rg	16.53 Å
total_rg	17.32 Å
total_atoms	1553
n_residues	186
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	58.1 Å
rg_real	17.42 Å
rg_real_error	0.24 Å
i0_real	1.6310e+07
i0_real_error	1.6760e+05
rg_reciprocal	17.43 Å
i0_reciprocal	16310000.0000
total_estimate	0.8822
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	21.7 Å
skewness	0.266
kurtosis	-0.286
angular_range	— – 0.4550 Å⁻¹
current_alpha	0.0002
highest_alpha	3816000.0000
n_real_points	76
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	1705

MGSSHHHHHHSSGLVPRGSHMASELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPCSLDKRVILIFHSEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSW

Source

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

Entity 2 non-polymer

description	;[(1~{R})-6'-methoxy-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl] dihydrogen phosphate ;
formula_weight	426.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	;[(1~{S})-6'-methoxy-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl] dihydrogen phosphate ;
formula_weight	426.3 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	119

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6. Citations (1)

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length_a	56.538 Å
length_b	66.318 Å
length_c	68.397 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	2.040 Å
resolution_low	43.610 Å
r_factor	0.1959
r_work	0.1949
r_free	0.2142

fit	/app/data/saxs_computation/t0/9t0a/9t0a.fit
pddf	/app/data/pr_computation/t0/9t0a/9t0a.pr.out
profile	/app/data/saxs_computation/t0/9t0a/9t0a.dat