2d2q

Crystal structure of the dimerized radixin FERM domain

Method: X-RAY DIFFRACTION Dmax: 109.3 Å Quality: GOOD

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

Radixin

Mus musculus

UniProt P26043

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 1–310 Fragment:FERM domain (residues 1-310) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;PEG 3350, HEPES-Na, pH 7.5, VAPOR DIFFUSION, temperature 293K Resolution 2.80 Å R-free 0.269
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–310 Fragment:FERM domain (residues 1-310) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 7.5;293 K;PEG 3350, HEPES-Na, pH 7.5, VAPOR DIFFUSION, temperature 293K Resolution 2.80 Å R-free 0.269

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 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RADI_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–310; UniProt 1–310 Author chain B; PDBConstruct 1–310; UniProt 1–310

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 2d2q

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2d2q
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2d2q
Deposition date deposition_date2005-09-15
Structure title titleCrystal structure of the dimerized radixin FERM domain
Keywords keywordsHomo dimer, Masking, CELL ADHESION; CELL ADHESION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.90
Radius of gyration Rg (electron density) rg_electron32.37
Forward intensity I(0) i074622800.00
Molecular weight molecular_weight70998.0 kDa
Excluded volume excluded_volume90010 ų
Envelope volume envelope_volume118470 ų
Hydration-shell volume shell_volume31855 ų
Envelope diameter envelope_diameter114.0
Shell Rg shell_rg37.47
Envelope Rg envelope_rg31.87
Shape Rg shape_rg32.37
Total Rg total_rg32.84
Total atoms total_atoms5016
Residues n_residues599
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 dmax109.3
Rg (real space) rg_real33.04
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real7.4620e+07
I(0) uncertainty (real space) i0_real_error1.0720e+06
Rg (reciprocal space) rg_reciprocal32.98
I(0) (reciprocal space) i0_reciprocal74620000.0000
Solution quality estimate total_estimate0.8882
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.7
Skewness Skewness skewness0.375
Kurtosis Kurtosis kurtosis-0.433
Angular range angular_range— – 0.2400 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha7391000.0000
Real-space data points n_real_points49
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.890

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd2d2qa1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd2d2qa2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd2d2qa3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches
Domain ID domain_idd2d2qb1
Class classa — All alpha proteins
Fold Fold folda.11 — Acyl-CoA binding protein-like
Superfamily Superfamily superfamilya.11.2 — Second domain of FERM
Family Family familya.11.2.0 — automated matches
Domain ID domain_idd2d2qb2
Class classb — All beta proteins
Fold Fold foldb.55 — PH domain-like barrel
Superfamily Superfamily superfamilyb.55.1 — PH domain-like
Family Family familyb.55.1.0 — automated matches
Domain ID domain_idd2d2qb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id2d2qA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2d2qA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id2d2qA03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id2d2qB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2d2qB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily10
Domain ID domain_id2d2qB03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

8. Citations (1)

9. Files and Curves (10)