SAXSdb — 3hqc

▼

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

Tensin-like C1 domain-containing 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 1264–1409	Fragment：Phosphotyrosine Binding Domain, PTB, residues 1264-1409 Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 ACT ACETATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4；294 K；100mM Sodium Acetate pH 4 + 2% Glycerol + 2000mM Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 1.80 Å R-free 0.242

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 3HQC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KNO NMR Solution Structure of SH2 Domain of the Human Tensin Like C1 Domain Containing Phosphatase (TENC1) Deposited 2009-08-27	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1135–1249（115 aa） Fragment：Src Homolog 2 domain of TENC1, UNP residues 1135-1249	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient NMR sample composition 1mM [U-100% 13C] SH2-1, 100mM sodium acetate-2, 100mM sodium chloride-3, 100% D2O \| 100% D2O NMR sample composition 1mM [U-100% 15N] SH2-4, 100mM sodium acetate-5, 100mM sodium chloride-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM [U-100% 13C; U-100% 15N] SH2-7, 100mM sodium acetate-8, 100mM sodium chloride-9, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM SH2-10, 100mM sodium acetate-11, 100mM sodium chloride-12, 100% D2O \| 100% D2O	Resolution not provided
2L6K Solution Structure of a Nonphosphorylated Peptide Recognizing Domain Deposited 2010-11-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1135–1248（114 aa） Fragment：Nonphosphorylated Peptide Recognizing Domain, SH2 domain, UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；293 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 0.6mM [U-99% 13C; U-99% 15N] Protein Domain; 150mM sodium chloride; 20mM sodium phosphate; 2mM EDTA; 50mM Arginine; 50mM glutamine; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LOZ The novel binding mode of DLC1 and Tensin2 PTB domain Deposited 2012-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1263–1409（147 aa） Fragment：PTB domain, UNP residues 1263-1409	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 0.6-0.8 mM [U-100% 13C; U-100% 15N] Tensin2-1, 1.2-1.4 mM DLC1-2, 100 mM potassium phosphate-3, 100 mM potassium chloride-4, 1 mM EDTA-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.2-1.4 mM Tensin2-6, 0.6-0.8 mM [U-100% 13C; U-100% 15N] DLC1-7, 100 mM potassium phosphate-8, 100 mM potassium chloride-9, 1 mM EDTA-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6-0.8 mM [U-100% 13C] Tensin2-11, 1.2-1.4 mM DLC1-12, 100 mM potassium phosphate-13, 100 mM potassium chloride-14, 1 mM EDTA-15, 100% D2O \| 100% D2O NMR sample composition 1.2-1.4 mM Tensin2-16, 0.6-0.8 mM [U-100% 13C] DLC1-17, 100 mM potassium phosphate-18, 100 mM potassium chloride-19, 1 mM EDTA-20, 100% D2O \| 100% D2O	Resolution not provided

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TENC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–149； UniProt 1264–1409

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	3hqc
Deposition date deposition_date	2009-06-05
Structure title title	Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1)
Keywords keywords	;Human Tensin-like C1 domain-containing phosphatase, TENC1, Phosphotyrosine Binding Domain, PTB, TNS2, KIAA1075, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, NEW YORK SGX Research Center for Structural Genomics, NYSGXRC, Cell junction, Cell membrane, Hydrolase, Membrane, Metal-binding, Phorbol-ester binding, Phosphoprotein, Protein phosphatase, SH2 domain, Zinc-finger ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	16.05 Å
Radius of gyration Rg (electron density) rg_electron	14.76 Å
Forward intensity I(0) i0	4985430.00
Molecular weight molecular_weight	15297.0 kDa
Excluded volume excluded_volume	18835 Å³
Envelope volume envelope_volume	22037 Å³
Hydration-shell volume shell_volume	12818 Å³
Envelope diameter envelope_diameter	52.6 Å
Shell Rg shell_rg	20.39 Å
Envelope Rg envelope_rg	15.20 Å
Shape Rg shape_rg	14.73 Å
Total Rg total_rg	15.92 Å
Total atoms total_atoms	1069
Residues n_residues	139
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	52.8 Å
Rg (real space) rg_real	15.95 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	4.9850e+06
I(0) uncertainty (real space) i0_real_error	5.6320e+04
Rg (reciprocal space) rg_reciprocal	15.96 Å
I(0) (reciprocal space) i0_reciprocal	4985000.0000
Solution quality estimate total_estimate	0.8781
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.145
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	735500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.985

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Tensin-like C1 domain-containing phosphatase
Molecular weight formula_weight	17310.2 kDa
EC 编号 ec_number	3.1.3.-
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	1229

MSLSTAADLLRQGAACSVLYLTSVETESLTGPQAVARASSAALSCSPRPTPAVVHFKVSAQGITLTDNQRKLFFRRHYPVNSITFSSTDPQDRRWTNPDGTTSKIFGFVAKKPGSPWENVCHLFAELDPDQPAGAIVTFITKVMLGQRKEGHHHHHH

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	3

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	79

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3hqca_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.2 — Phosphotyrosine-binding domain (PTB)

CATH v4.4 (1 domains)

Domain ID domain_id	3hqcA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

▶

8. Citations (1)

▶

Unit-cell length a length_a	108.909 Å
Unit-cell length b length_b	108.909 Å
Unit-cell length c length_c	36.196 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	26.160 Å
R factor r_factor	0.2140
R_work r_work	0.2120
R_free r_free	0.2420

fit	/app/data/saxs_computation/hq/3hqc/3hqc.fit
pddf	/app/data/pr_computation/hq/3hqc/3hqc.pr.out
profile	/app/data/saxs_computation/hq/3hqc/3hqc.dat

Crystal structure of Phosphotyrosine-binding domain from the Human Tensin-like C1 domain-containing phosphatase (TENC1)

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

Tensin-like C1 domain-containing phosphatase

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