SAXSdb — 2b3o

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

Tyrosine-protein phosphatase, non-receptor type 6

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 1–532	Fragment：SHP-1	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 800, DTT, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.296

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 2B3O	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FPR CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1. Deposited 2000-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 243–526（284 aa） Fragment：CATALYTIC DOMAIN	Mutation：C455S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.50 Å R-free 0.303
1FPR CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1. Deposited 2000-08-31	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 243–526（284 aa） Fragment：CATALYTIC DOMAIN	Mutation：C455S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.50 Å R-free 0.303
1GWZ CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE PROTEIN TYROSINE PHOSPHATASE SHP-1 Deposited 1998-08-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–541（299 aa） Fragment：CATALYTIC DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.50 Å R-free 0.293
1X6C Solution structures of the SH2 domain of human protein-tyrosine phosphatase SHP-1 Deposited 2005-05-17	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–214（105 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1mM SH2 domain U-15N, 13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RMX Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Deposited 2007-11-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–214（105 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.8mM [U-13C; U-15N] SHP-1 C-terminal SH2 domain; 0.8mM tyrosine-phosphorylated peptide; 20mM [U-2H] TRIS; 100mM sodium chloride; 0.02% sodium azide; 1mM [U-2H] DTT; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YU7 Solution structure of the SHP-1 C-terminal SH2 domain complexed with a tyrosine-phosphorylated peptide from NKG2A Deposited 2007-04-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–214（105 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.89mM SHP1 SH2 domain U-15N,13C; 0.89mM NKG2A peptide; 20mM d-Tris-HCl (pH 7.4); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3PS5 Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1 Deposited 2010-11-30	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 1–595（595 aa）	Mutation：C453S	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy Big Chap to form the final drop., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 3.10 Å R-free 0.276
3PS5 Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1 Deposited 2010-11-30	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 A 1–595（595 aa）	Mutation：C453S	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；278 K；2.5 ul of SHP-1 at 3.5 mg/ml in 25mM Tris-HCl, beta-mercaptoethanol, 1mM EDTA mixed with 2.5 ul of 1.8M ammonium sulfate, 0.1M glycine, 0.1M Tris-HCl, with the addition of 0.5 ul 14mM deoxy Big Chap to form the final drop., pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 3.10 Å R-free 0.276
4GRY Crystal structure of SHP1 catalytic domain with SO4 Deposited 2012-08-27	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 243–528（286 aa） Fragment：Phosphatase domain UNP Residues 242-528	Mutation：C453S	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M MES pH 6.5, 1.5 M ammonium sulfate, 3% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.231
4GRZ Crystal structure of SHP1 catalytic domain with PO4 Deposited 2012-08-27	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 243–528（286 aa） Fragment：Phosphatase domain UNP Residues 242-528	Mutation：C453S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M ammonium phosphate, 12% PEG2000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.37 Å R-free 0.189
4GS0 Crystal structure of SHP1 catalytic domain with JAK1 activation loop peptide Deposited 2012-08-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M calcium acetate, 13% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.195
4GS0 Crystal structure of SHP1 catalytic domain with JAK1 activation loop peptide Deposited 2012-08-27	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.2 M calcium acetate, 13% PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.195
4HJP SHP-1 catalytic domain WPD loop open Deposited 2012-10-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH 7.5, 1.0 M tri-sodium citrate, 2-4% 1-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.186
4HJQ SHP-1 catalytic domain WPD loop closed Deposited 2012-10-13	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 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Mutation：C453S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH7.5, 20 mM MgCl2, 28% sodium polyacrylate 5100 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
4HJQ SHP-1 catalytic domain WPD loop closed Deposited 2012-10-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 243–528（286 aa） Fragment：Phosphatase domain (UNP Residues 242-528)	Mutation：C453S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES pH7.5, 20 mM MgCl2, 28% sodium polyacrylate 5100 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.202
6SM5 MbC/SHP1-C-SH2 complex Deposited 2019-08-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 100–214（115 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M sodium citrate tribasic, 0.1 M bistros propane 8.4 and 20 % PEG 3350	Resolution 2.75 Å R-free 0.276
8YHI The Crystal Structure of SHP1 from Biortus. Deposited 2024-02-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–528（286 aa）	Not recorded	SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M Hepes pH7.5, 2% PEG 400, 2.0M (NH4)2SO4	Resolution 1.75 Å R-free 0.227

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTN6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–532； UniProt 1–532

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	2b3o
Deposition date deposition_date	2005-09-20
Structure title title	Crystal structure of human tyrosine phosphatase SHP-1
Keywords keywords	Protein Tyrosine Phosphatase, SHP-1, Signaling, HYDROLASE; HYDROLASE
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	26.46 Å
Radius of gyration Rg (electron density) rg_electron	25.64 Å
Forward intensity I(0) i0	56249400.00
Molecular weight molecular_weight	57340.0 kDa
Excluded volume excluded_volume	71358 Å³
Envelope volume envelope_volume	88127 Å³
Hydration-shell volume shell_volume	29186 Å³
Envelope diameter envelope_diameter	92.5 Å
Shell Rg shell_rg	32.45 Å
Envelope Rg envelope_rg	25.86 Å
Shape Rg shape_rg	25.63 Å
Total Rg total_rg	26.40 Å
Total atoms total_atoms	4043
Residues n_residues	504
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	89.0 Å
Rg (real space) rg_real	26.47 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	5.6250e+07
I(0) uncertainty (real space) i0_real_error	7.3400e+05
Rg (reciprocal space) rg_reciprocal	26.47 Å
I(0) (reciprocal space) i0_reciprocal	56250000.0000
Solution quality estimate total_estimate	0.8818
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.384
Kurtosis Kurtosis kurtosis	-0.305
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17110000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein phosphatase, non-receptor type 6
Molecular weight formula_weight	60350.7 kDa
EC 编号 ec_number	3.1.3.48
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	4062

MVRWFHRDLSGLDAETLLKGRGVHGSFLARPSRKNQGDFSLSVRVGDQVTHIRIQNSGDFYDLYGGEKFATLTELVEYYTQQQGVLQDRDGTIIHLKYPLNCSDPTSERWYHGHMSGGQAETLLQAKGEPWTFLVRESLSQPGDFVLSVLSDQPKAGPGSPLRVTHIKVMCEGGRYTVGGLETFDSLTDLVEHFKKTGIEEASGAFVYLRQPYYATRVNAADIENRVLELNKKQESEDTAKAGFWEEFESLQKQEVKNLHQRLEGQRPENKGKNRYKNILPFDHSRVILQGRDSNIPGSDYINANYIKNQLLGPDENAKTYIASQGCLEATVNDFWQMAWQENSRVIVMTTREVEKGRNKCVPYWPEVGMQRAYGPYSVTNCGEHDTTEYKLRTLQVSPLDNGDLIREIWHYQYLSWPDHGVPSEPGGVLSFLDQINQRQESLPHAGPIIVHCSAGIGRTGTIIVIDMLMENISTKGLDCDIDIQKTIQMVRAQRSGMVQTEAQYKFIYVAIAQFIETTKKKLEVLQSQKGQ

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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2b3oa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.0 — automated matches

Domain ID domain_id	d2b3oa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.0 — automated matches

Domain ID domain_id	d2b3oa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.45 — (Phosphotyrosine protein) phosphatases II
Superfamily Superfamily superfamily	c.45.1 — (Phosphotyrosine protein) phosphatases II
Family Family family	c.45.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	2b3oA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	2b3oA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

Domain ID domain_id	2b3oA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	190 — Protein-Tyrosine Phosphatase; Chain A
Homologous superfamily homologous superfamily	10 — Protein tyrosine phosphatase superfamily

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8. Citations (1)

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Unit-cell length a length_a	44.736 Å
Unit-cell length b length_b	100.404 Å
Unit-cell length c length_c	149.475 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	2.800 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2410
R_work r_work	0.2330
R_free r_free	0.2960

fit	/app/data/saxs_computation/b3/2b3o/2b3o.fit
pddf	/app/data/pr_computation/b3/2b3o/2b3o.pr.out
profile	/app/data/saxs_computation/b3/2b3o/2b3o.dat

Crystal structure of human tyrosine phosphatase SHP-1

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

Tyrosine-protein phosphatase, non-receptor type 6

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