SAXSdb — 2ixm

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

;SERINE/THREONINE-PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT B' ;

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 20–322	Fragment：RESIDUES 20-322	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PTPA CRYSTALS WERE GROWN USING THE HANGING DROP METHOD AT 20C. 1UL OF PROTEIN (20 MG/ML) WAS MIXED WITH 1 UL OF PRECIPITANT (23% TO 28% PEG 4000, 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 7.0-8.5 AND 5 MM DTT) WERE EQUILIBRATED AGAINST 0.5 ML OF PRECIPITANT. LARGE PLATE CRYSTALS APPEARED IN 2 TO 3 DAYS. FOR CRYOPROTECTION 5% MPD WAS ADDED TO THE PRECIPITANT SOLUTION.	Resolution 1.50 Å R-free 0.221

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 2IXM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2G62 Crystal structure of human PTPA Deposited 2006-02-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 22–358（337 aa）	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.183
2HV6 Crystal structure of the phosphotyrosyl phosphatase activator Deposited 2006-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–323（323 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2mM Mg Formate, 5% glycerol, 17.5% PEG3350 (w/v), 0.1 M Bistris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.239
2HV6 Crystal structure of the phosphotyrosyl phosphatase activator Deposited 2006-07-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–323（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2mM Mg Formate, 5% glycerol, 17.5% PEG3350 (w/v), 0.1 M Bistris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.239
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–323（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–323（323 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–323（323 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–323（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–323（323 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–323（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1–323（323 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
2HV7 Crystal structure of phosphotyrosyl phosphatase activator bound to ATPgammaS Deposited 2006-07-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1–323（323 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；0.2 mM Na Formate, 5% glycerol, 16% PEG3350 (w/v), 50 mM Glycine, 0.1 M BisTris, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.312
4LAC Crystal Structure of Protein Phosphatase 2A (PP2A) and PP2A phosphatase activator (PTPA) complex with ATPgammaS Deposited 2013-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 19–358（340 aa） Fragment：unp residues 19-358	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 MN MANGANESE (II) ION × 2 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1M MES at pH6.5 and 10-12% PEG20,000, 1mM ATPgammaS, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.82 Å R-free 0.242
4NY3 Human PTPA in complex with peptide Deposited 2013-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 22–323（302 aa） Fragment：UNP Residues 22-323	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；2 M (NH4)2SO4 and 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.185
4NY3 Human PTPA in complex with peptide Deposited 2013-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–323（302 aa） Fragment：UNP Residues 22-323	Not recorded	SO4 SULFATE ION × 5 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；2 M (NH4)2SO4 and 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.185

5 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTPA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–303； UniProt 20–322

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	2ixm
Deposition date deposition_date	2006-07-09
Structure title title	Structure of human PTPA
Keywords keywords	PROTEIN PHOSPHATASE 2A, 2 PTPA, PPIASE, HYDROLASE ACTIVATOR; HYDROLASE ACTIVATOR
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	20.08 Å
Radius of gyration Rg (electron density) rg_electron	18.79 Å
Forward intensity I(0) i0	18648100.00
Molecular weight molecular_weight	34393.0 kDa
Excluded volume excluded_volume	43706 Å³
Envelope volume envelope_volume	49362 Å³
Hydration-shell volume shell_volume	21423 Å³
Envelope diameter envelope_diameter	63.8 Å
Shell Rg shell_rg	25.70 Å
Envelope Rg envelope_rg	19.10 Å
Shape Rg shape_rg	18.79 Å
Total Rg total_rg	19.79 Å
Total atoms total_atoms	2431
Residues n_residues	300
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	60.2 Å
Rg (real space) rg_real	19.93 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	1.8650e+07
I(0) uncertainty (real space) i0_real_error	2.0890e+05
Rg (reciprocal space) rg_reciprocal	19.96 Å
I(0) (reciprocal space) i0_reciprocal	18650000.0000
Solution quality estimate total_estimate	0.9067
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.064
Kurtosis Kurtosis kurtosis	-0.525
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4411000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ixma1
Class class	a — All alpha proteins
Fold Fold fold	a.268 — PTPA-like
Superfamily Superfamily superfamily	a.268.1 — PTPA-like
Family Family family	a.268.1.1 — PTPA-like

CATH v4.4 (1 domains)

Domain ID domain_id	2ixmA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1150 — Phosphotyrosyl phosphate activator, C-terminal lid domain

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8. Citations (1)

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Unit-cell length a length_a	48.243 Å
Unit-cell length b length_b	70.410 Å
Unit-cell length c length_c	95.534 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	1.500 Å
Low-resolution limit resolution_low	56.700 Å
R factor r_factor	0.2030
R_work r_work	0.2020
R_free r_free	0.2210

Description description	;SERINE/THREONINE-PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT B' ;
Molecular weight formula_weight	34798.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2681

Structure of human PTPA

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

;SERINE/THREONINE-PROTEIN PHOSPHATASE 2A REGULATORY SUBUNIT B' ;

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	242

fit	/app/data/saxs_computation/ix/2ixm/2ixm.fit
pddf	/app/data/pr_computation/ix/2ixm/2ixm.pr.out
profile	/app/data/saxs_computation/ix/2ixm/2ixm.dat