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4kee

Crystal Structure of Cofilin Mutant (cof1-158p)

Method: X-RAY DIFFRACTION Dmax: 53.3 Å Quality: GOOD
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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：R80E No other associated polymer 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

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 4KEE 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
4KED Crystal Structure of Cofilin Mutant (cof1-157p) 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：R135D 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 1.90 Å R-free 0.233
4KED Crystal Structure of Cofilin Mutant (cof1-157p) Deposited 2013-04-25 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 2–143（142 aa）
Mutation：R135D 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 1.90 Å R-free 0.233
4KEF Structure of Cofilin Mutant (cof1-159p) 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：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 7 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

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 4kee

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4kee
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4kee
Deposition date deposition_date2013-04-25
Structure title titleCrystal Structure of Cofilin Mutant (cof1-158p)
Keywords keywordsActin Depolymerization Factor, Actin Binding Protein; Actin Binding Protein
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.92 Å
Radius of gyration Rg (electron density) rg_electron14.28 Å
Forward intensity I(0) i04234000.00
Molecular weight molecular_weight14711.0 kDa
Excluded volume excluded_volume18452 ų
Envelope volume envelope_volume21193 ų
Hydration-shell volume shell_volume12591 ų
Envelope diameter envelope_diameter54.0 Å
Shell Rg shell_rg20.15 Å
Envelope Rg envelope_rg14.82 Å
Shape Rg shape_rg14.23 Å
Total Rg total_rg15.65 Å
Total atoms total_atoms2005
Residues n_residues132
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax53.3 Å
Rg (real space) rg_real15.84 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real4.2340e+06
I(0) uncertainty (real space) i0_real_error5.3490e+04
Rg (reciprocal space) rg_reciprocal15.85 Å
I(0) (reciprocal space) i0_reciprocal4234000.0000
Solution quality estimate total_estimate0.7857
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.9 Å
Skewness Skewness skewness0.192
Kurtosis Kurtosis kurtosis-0.219
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1021000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4keea1
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_idd4keea2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id4keeA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology20 — Severin
Homologous superfamily homologous superfamily10 — Severin
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8. Citations (1)

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9. Files and Curves (10)