SAXSdb — 2g62

▼

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

;protein phosphatase 2A, regulatory subunit B' (PR 53) ;

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 22–358	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.60 Å R-free 0.183

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 2G62	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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	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 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	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 ligand/ion 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 ligand/ion 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 ligand/ion 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
2IXM Structure of human PTPA Deposited 2006-07-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–322（303 aa） Fragment：RESIDUES 20-322	Not recorded	No recorded non-water small molecule	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
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 24–325； UniProt 22–358

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2g62
Deposition date deposition_date	2006-02-24
Structure title title	Crystal structure of human PTPA
Keywords keywords	;PPP2R4, MGC2184, PP2A, PR53, PTPA, protein phosphatase 2A, regulatory subunit B' (PR 53), HYDROLASE ACTIVATOR ;; HYDROLASE ACTIVATOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.54 Å
Radius of gyration Rg (electron density) rg_electron	19.14 Å
Forward intensity I(0) i0	20340700.00
Molecular weight molecular_weight	35265.0 kDa
Excluded volume excluded_volume	44529 Å³
Envelope volume envelope_volume	50150 Å³
Hydration-shell volume shell_volume	21476 Å³
Envelope diameter envelope_diameter	64.8 Å
Shell Rg shell_rg	25.95 Å
Envelope Rg envelope_rg	19.51 Å
Shape Rg shape_rg	19.13 Å
Total Rg total_rg	20.12 Å
Total atoms total_atoms	2485
Residues n_residues	302
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

▼

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

Maximum dimension Dmax dmax	63.6 Å
Rg (real space) rg_real	20.40 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.0340e+07
I(0) uncertainty (real space) i0_real_error	2.5310e+05
Rg (reciprocal space) rg_reciprocal	20.43 Å
I(0) (reciprocal space) i0_reciprocal	20340000.0000
Solution quality estimate total_estimate	0.6874
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.7 Å
Skewness Skewness skewness	0.105
Kurtosis Kurtosis kurtosis	-0.475
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5137000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 0.072; Positv: 1.000; Valcen: 0.985; Smooth: 0.999

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	;protein phosphatase 2A, regulatory subunit B' (PR 53) ;
Molecular weight formula_weight	37327.8 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	2944

MHHHHHHSSGVDLGTENLYFQSRNFIIPKKEIHTVPDMGKWKRSQAYADYIGFILTLNEGVKGKKLTFEYRVSEAIEKLVALLNTLDRWIDETPPVDQPSRFGNKAYRTWYAKLDEEAENLVATVVPTHLAAAVPEVAVYLKESVGNSTRIDYGTGHEAAFAAFLCCLCKIGVLRVDDQIAIVFKVFNRYLEVMRKLQKTYRMEPAGSQGVWGLDDFQFLPFIWGSSQLIDHPYLEPRHFVDEKAVNENHKDYMFLECILFITEMKTGPFAEHSNQLWNISAVPSWSKVNQGLIRMYKAECLEKFPVIQHFKFGSLLPIHPVTSG

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	417

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2g62a1
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

Domain ID domain_id	d2g62a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2g62A02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	48.190 Å
Unit-cell length b length_b	76.420 Å
Unit-cell length c length_c	87.300 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	1.600 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.1536
R_work r_work	0.1520
R_free r_free	0.1834

fit	/app/data/saxs_computation/g6/2g62/2g62.fit
pddf	/app/data/pr_computation/g6/2g62/2g62.pr.out
profile	/app/data/saxs_computation/g6/2g62/2g62.dat

Crystal structure of human PTPA