1rpy

CRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS

Method: X-RAY DIFFRACTION Dmax: 53.9 Å Quality: GOOD

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

adaptor protein APS

Rattus norvegicus

UniProt Q9Z200

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 401–510 Chain B; UniProt 401–510 Fragment:SH2 domain Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;Ammonium sulfate/tris, pH 7.5, pH 7.50 Resolution 2.30 Å R-free 0.270
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 401–510 Chain B; UniProt 401–510 Fragment:SH2 domain Non-standard monomer:Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;Ammonium sulfate/tris, pH 7.5, pH 7.50 Resolution 2.30 Å R-free 0.270

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APS_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–114; UniProt 401–510 Author chain B; PDBConstruct 5–114; UniProt 401–510

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 1rpy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1rpy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1rpy
Deposition date deposition_date2003-12-03
Structure title titleCRYSTAL STRUCTURE OF THE DIMERIC SH2 DOMAIN OF APS
Keywords keywordsADAPTER PROTEIN, SH2 DOMAIN, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.00
Radius of gyration Rg (electron density) rg_electron15.71
Forward intensity I(0) i07333390.00
Molecular weight molecular_weight19477.0 kDa
Excluded volume excluded_volume24233 ų
Envelope volume envelope_volume27805 ų
Hydration-shell volume shell_volume14870 ų
Envelope diameter envelope_diameter55.2
Shell Rg shell_rg21.62
Envelope Rg envelope_rg16.08
Shape Rg shape_rg15.66
Total Rg total_rg16.90
Total atoms total_atoms1370
Residues n_residues166
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 dmax53.9
Rg (real space) rg_real16.88
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real7.3330e+06
I(0) uncertainty (real space) i0_real_error8.9690e+04
Rg (reciprocal space) rg_reciprocal16.90
I(0) (reciprocal space) i0_reciprocal7333000.0000
Solution quality estimate total_estimate0.8169
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.0
Skewness Skewness skewness0.070
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.4700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha982800.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1rpya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain
Domain ID domain_idd1rpyb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.93 — SH2-like
Superfamily Superfamily superfamilyd.93.1 — SH2 domain
Family Family familyd.93.1.1 — SH2 domain

CATH v4.4 (2 domains)

Domain ID domain_id1rpyA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain
Domain ID domain_id1rpyB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily10 — SH2 domain

8. Citations (1)

9. Files and Curves (10)