SAXSdb — 1cws

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CDC25 B-TYPE TYROSINE PHOSPHATASE

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 329–539	Fragment：CATALYTIC DOMAIN	WO4 TUNGSTATE(VI)ION × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 9；4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, WO4=,1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C	Resolution 2.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1CWS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CWR HUMAN CDC25B CATALYTIC DOMAIN WITHOUT ION IN CATALYTIC SITE Deposited 1999-08-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 356–566（211 aa） Fragment：CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C	Resolution 2.10 Å
1CWT HUMAN CDC25B CATALYTIC DOMAIN WITH METHYL MERCURY Deposited 1999-08-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 347–524（178 aa） Fragment：CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 MMC METHYL MERCURY ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, CH(3)HGCL,1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C	Resolution 2.30 Å
1QB0 HUMAN CDC25B CATALYTIC DOMAIN Deposited 1999-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 356–566（211 aa） Fragment：CATALYTIC DOMAIN	Not recorded	SO4 SULFATE ION × 2 CL CHLORIDE ION × 1 BME BETA-MERCAPTOETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；4 MICROLITERS PROTEIN (10 MG/ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C, VAPOR DIFFUSION, SITTING DROP, temperature 4.0K	Resolution 1.91 Å
1YM9 Crystal structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfinic form Deposited 2005-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：catalytic domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 2.00 Å R-free 0.237
1YMD Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfonic form Deposited 2005-01-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：catalytic domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 1.70 Å R-free 0.209
1YMK Crystal Structure of the CDC25B phosphatase catalytic domain in the apo form Deposited 2005-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：catalytic domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT,Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 1.70 Å R-free 0.196
1YML Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the sulfenic form Deposited 2005-01-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：catalytic domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT,Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 1.70 Å R-free 0.208
1YS0 Crystal Structure of the CDC25B phosphatase catalytic domain with the active site cysteine in the disulfide form Deposited 2005-02-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：catalytic domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；DTT, Tris, Ammonium Sulfate, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 100.0K	Resolution 2.00 Å R-free 0.244
2A2K Crystal Structure of an active site mutant, C473S, of Cdc25B Phosphatase Catalytic Domain Deposited 2005-06-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 377–550（174 aa） Fragment：Catalytic Domain	Mutation：C473S	CL CHLORIDE ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；DTT, Ammonium Sulfate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.52 Å R-free 0.191
2IFD Crystal structure of a remote binding site mutant, R492L, of CDC25B Phosphatase catalytic domain Deposited 2006-09-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：CATALYTIC DOMAIN, residues 391-564	Mutation：R492L	SO4 SULFATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；DTT, AMMONIUM SULFATE, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.00 Å R-free 0.212
2IFV Crystal structure of an active site mutant, C473D, of CDC25B phosphatase catalytic domain Deposited 2006-09-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa） Fragment：Catalytic domain, residues 391-564	Mutation：C473D	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；DTT, AMMONIUM SULFATE, TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.60 Å R-free 0.192
2UZQ Protein Phosphatase, New Crystal Form Deposited 2007-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566 Chain B 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE	Resolution 2.38 Å R-free 0.249
2UZQ Protein Phosphatase, New Crystal Form Deposited 2007-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566 Chain D 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE	Resolution 2.38 Å R-free 0.249
2UZQ Protein Phosphatase, New Crystal Form Deposited 2007-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566 Chain F 377–566（190 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 377-566	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE	Resolution 2.38 Å R-free 0.249
4WH7 Structure of the CDC25B Phosphatase Catalytic Domain with Bound Ligand Deposited 2014-09-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 386–565（180 aa） Fragment：catalytic domain (UNP residues 386-565)	Mutation：C473S	SO4 SULFATE ION × 6 8H8 2-fluoro-4-hydroxybenzonitrile × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；(NH4)2SO4, Tris, TCEP	Resolution 1.62 Å R-free 0.198
4WH9 Structure of the CDC25B Phosphatase Catalytic Domain with Bound Inhibitor Deposited 2014-09-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 386–565（180 aa） Fragment：catalytic domain (UNP residues 386-565)	Mutation：C473S	3M8 2-[(2-cyano-3-fluoro-5-hydroxyphenyl)sulfanyl]ethanesulfonic acid × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；(NH4)2SO4, Tris, TCEP	Resolution 1.50 Å R-free 0.152
9T09 X-ray structure of the catalytic domain of CDC25B C473S at 1.34 angstrom resolution Deposited 2025-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa）	Mutation：C473S	SO4 SULFATE ION × 4 CL CHLORIDE ION × 1 ZN ZINC ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2.0 M ammonium sulphate, 0.5 M NaCl, 0.1 M Tris-HCl pH 7.5, and 0.5 mM TCEP	Resolution 1.34 Å R-free 0.175
9T0A X-ray structure of the complex between the catalytic domain of CDC25B C473S and 3-O-methylfluorescein phosphate (3-OMFP) Deposited 2025-10-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–564（174 aa）	Mutation：C473S	A1JSQ [(1~{R})-6'-methoxy-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl] dihydrogen phosphate × 1 A1JSP [(1~{S})-6'-methoxy-3-oxidanylidene-spiro[2-benzofuran-1,9'-xanthene]-3'-yl] dihydrogen phosphate × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；3.8 M NaCl, 0.1 M HEPES pH 7.5, and 1.2% v/v 2-propanol	Resolution 2.04 Å R-free 0.214

16 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MPIP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 329–539

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cws
Deposition date deposition_date	1999-08-26
Structure title title	HUMAN CDC25B CATALYTIC DOMAIN WITH TUNGSTATE
Keywords keywords	HYDROLASE, CELL CYCLE PHOSPHATASE, DUAL SPECIFICITY PROTEIN PHOSPHATASE, CDC25, CDC25B, CELL CYCLE; CELL CYCLE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	17.48 Å
Radius of gyration Rg (electron density) rg_electron	16.39 Å
Forward intensity I(0) i0	8741740.00
Molecular weight molecular_weight	21472.0 kDa
Excluded volume excluded_volume	26654 Å³
Envelope volume envelope_volume	30486 Å³
Hydration-shell volume shell_volume	15665 Å³
Envelope diameter envelope_diameter	57.7 Å
Shell Rg shell_rg	22.47 Å
Envelope Rg envelope_rg	16.79 Å
Shape Rg shape_rg	16.43 Å
Total Rg total_rg	17.28 Å
Total atoms total_atoms	1497
Residues n_residues	179
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	59.0 Å
Rg (real space) rg_real	17.41 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	8.7420e+06
I(0) uncertainty (real space) i0_real_error	1.0350e+05
Rg (reciprocal space) rg_reciprocal	17.42 Å
I(0) (reciprocal space) i0_reciprocal	8742000.0000
Solution quality estimate total_estimate	0.7979
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.240
Kurtosis Kurtosis kurtosis	-0.265
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1651000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	CDC25 B-TYPE TYROSINE PHOSPHATASE
Molecular weight formula_weight	24907.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1666

VLRSKSLCHDEIENLLDSDHRELIGDYSKAFLLQTVDGKHQDLKYISPETMVALLTGKFSNIVDKFVIVDCRYPYEYEGGHIKTAVNLPLERDAESFLLKSPIAPCSLDKRVILIFHCEFSSERGPRMCRFIRERDRAVNDYPSLYYPEMYILKGGYKEFFPQHPNFCEPQDYRPMNHEAFKDELKTFRLKTRSWAGERSRRELCSRLQDQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	TUNGSTATE(VI)ION
Molecular weight formula_weight	247.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	163

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cwsa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.46 — Rhodanese/Cell cycle control phosphatase
Superfamily Superfamily superfamily	c.46.1 — Rhodanese/Cell cycle control phosphatase
Family Family family	c.46.1.1 — Cell cycle control phosphatase, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id	1cwsA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	250 — Oxidized Rhodanese; domain 1
Homologous superfamily homologous superfamily	10 — Rhodanese-like domain

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8. Citations (1)

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Unit-cell length a length_a	51.734 Å
Unit-cell length b length_b	71.863 Å
Unit-cell length c length_c	74.935 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1680
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/cw/1cws/1cws.fit
pddf	/app/data/pr_computation/cw/1cws/1cws.pr.out
profile	/app/data/saxs_computation/cw/1cws/1cws.dat

HUMAN CDC25B CATALYTIC DOMAIN WITH TUNGSTATE