5lm2

Crystal Structure of HD-PTP phosphatase

Method: X-RAY DIFFRACTION Dmax: 136.7 Å Quality: REASONABLE

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

Tyrosine-protein phosphatase non-receptor type 23

Homo sapiens

UniProt Q9H3S7

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 362–713 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;294 K;0.1 M Bis-Tris pH 6.0, 0.1-0.2 M Na-Formate and 13-15% PEG3350 Resolution 2.54 Å R-free 0.271
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 362–713 Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;294 K;0.1 M Bis-Tris pH 6.0, 0.1-0.2 M Na-Formate and 13-15% PEG3350 Resolution 2.54 Å R-free 0.271

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.

10 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PTN23_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–352; UniProt 362–713 Author chain B; PDBConstruct 1–352; UniProt 362–713

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5lm2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5lm2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5lm2
Deposition date deposition_date2016-07-28
Structure title titleCrystal Structure of HD-PTP phosphatase
Keywords keywordscoiled coil, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.15
Radius of gyration Rg (electron density) rg_electron55.34
Forward intensity I(0) i094480300.00
Molecular weight molecular_weight75813.0 kDa
Excluded volume excluded_volume93422 ų
Envelope volume envelope_volume156160 ų
Hydration-shell volume shell_volume29562 ų
Envelope diameter envelope_diameter222.3
Shell Rg shell_rg41.64
Envelope Rg envelope_rg56.94
Shape Rg shape_rg55.22
Total Rg total_rg55.04
Total atoms total_atoms5240
Residues n_residues636
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax136.7
Rg (real space) rg_real47.49
Rg uncertainty (real space) rg_real_error0.62
I(0) (real space) i0_real8.9440e+07
I(0) uncertainty (real space) i0_real_error1.4540e+06
Rg (reciprocal space) rg_reciprocal52.20
I(0) (reciprocal space) i0_reciprocal94200000.0000
Solution quality estimate total_estimate0.6535
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9
Skewness Skewness skewness0.291
Kurtosis Kurtosis kurtosis-0.825
Angular range angular_range— – 0.1500 −1
Current regularization parameter α current_alpha0.5423
Highest regularization parameter α highest_alpha2277000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.016; Oscil: 0.955; Stabil: 0.990; Sysdev: 0.000; Positv: 1.000; Valcen: 0.662; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)