← Back to search
4ked

Crystal Structure of Cofilin Mutant (cof1-157p)

Method: X-RAY DIFFRACTION Dmax: 75.9 Å Quality: GOOD
▼

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

Cofilin

Saccharomyces cerevisiae

UniProt Q03048

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 2–143 Mutation：R135D No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；20% PEG4000, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.90 Å R-free 0.233
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 2–143 Mutation：R135D No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；20% PEG4000, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 1.90 Å R-free 0.233

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 4KED Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CFY YEAST COFILIN, MONOCLINIC CRYSTAL FORM Deposited 1996-11-26 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–143（143 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；CRYSTALLIZED FROM 30% PEG 4000 SOLUTION., pH 7.2
Resolution 2.30 Å
1CFY YEAST COFILIN, MONOCLINIC CRYSTAL FORM Deposited 1996-11-26 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–143（143 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；CRYSTALLIZED FROM 30% PEG 4000 SOLUTION., pH 7.2
Resolution 2.30 Å
1COF YEAST COFILIN, ORTHORHOMBIC CRYSTAL FORM Deposited 1996-11-26 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–143（143 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；CRYSTALLIZED FROM 25% PEG 4000 SOLUTION., pH 7.2
Resolution 2.30 Å
1QPV YEAST COFILIN Deposited 1999-05-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–143（143 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；PEG 4000 , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 3.00 Å R-free 0.284
4KEE Crystal Structure of Cofilin Mutant (cof1-158p) Deposited 2013-04-25 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–143（142 aa）
Mutation：R80E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；20% PEG 4000, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.45 Å R-free 0.175
4KEF Structure of Cofilin Mutant (cof1-159p) Deposited 2013-04-25 Different mutation/modification Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–143（142 aa）
Mutation：K82D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；20% PEG4000, 150mM NaCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.10 Å R-free 0.144

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COFI_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–143； UniProt 2–143 Author chain B； PDBConstruct 2–143； UniProt 2–143

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 4ked

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ked
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id4ked
Deposition date deposition_date2013-04-25
Structure title titleCrystal Structure of Cofilin Mutant (cof1-157p)
Keywords keywordsActin Depolymerization Factor, Actin Binding Protein; Actin Binding Protein
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier22.86 Å
Radius of gyration Rg (electron density) rg_electron22.20 Å
Forward intensity I(0) i014507700.00
Molecular weight molecular_weight29331.0 kDa
Excluded volume excluded_volume36912 ų
Envelope volume envelope_volume44916 ų
Hydration-shell volume shell_volume17876 ų
Envelope diameter envelope_diameter78.4 Å
Shell Rg shell_rg27.32 Å
Envelope Rg envelope_rg22.24 Å
Shape Rg shape_rg22.16 Å
Total Rg total_rg23.02 Å
Total atoms total_atoms2072
Residues n_residues262
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax75.9 Å
Rg (real space) rg_real22.95 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real1.4510e+07
I(0) uncertainty (real space) i0_real_error2.1140e+05
Rg (reciprocal space) rg_reciprocal22.93 Å
I(0) (reciprocal space) i0_reciprocal14510000.0000
Solution quality estimate total_estimate0.7964
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.2 Å
Skewness Skewness skewness0.424
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3914000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.817; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.901; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4keda_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.109 — Gelsolin-like
Superfamily Superfamily superfamilyd.109.1 — Actin depolymerizing proteins
Family Family familyd.109.1.2 — Cofilin-like
Domain ID domain_idd4kedb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.109 — Gelsolin-like
Superfamily Superfamily superfamilyd.109.1 — Actin depolymerizing proteins
Family Family familyd.109.1.2 — Cofilin-like

CATH v4.4 (2 domains)

Domain ID domain_id4kedA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin
Domain ID domain_id4kedB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin
▶

8. Citations (1)

▶

9. Files and Curves (10)