3u4l

Cryocooled bovine profilin:actin crystal structure to 2.4 A

Method: X-RAY DIFFRACTION Dmax: 88.7 Å Quality: REASONABLE

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

Actin, cytoplasmic 1

OrganismNot specified

UniProt P60712

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–375 Not recorded Profilin-1 × 1 (P02584) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.3;277 K;1.3M KPO4, 0.5 mM ATP, 0.2 mM CaCl2, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.331

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.

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

View Construct and Data Evidence
UniProt name ACTB_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–375; UniProt 1–375

Profilin-1

OrganismNot specified

UniProt P02584

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 2–140 Non-standard monomer:Yes (specific site not provided by mmCIF) Actin, cytoplasmic 1 × 1 (P60712) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.3;277 K;1.3M KPO4, 0.5 mM ATP, 0.2 mM CaCl2, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 2.40 Å R-free 0.331

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.

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PROF1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain P; PDBConstruct 2–140; UniProt 2–140

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 3u4l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3u4l
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3u4l
Deposition date deposition_date2011-10-09
Structure title titleCryocooled bovine profilin:actin crystal structure to 2.4 A
Keywords keywordsATPase, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.46
Radius of gyration Rg (electron density) rg_electron24.76
Forward intensity I(0) i049986400.00
Molecular weight molecular_weight54079.0 kDa
Excluded volume excluded_volume67293 ų
Envelope volume envelope_volume81098 ų
Hydration-shell volume shell_volume27779 ų
Envelope diameter envelope_diameter90.1
Shell Rg shell_rg31.82
Envelope Rg envelope_rg25.07
Shape Rg shape_rg24.79
Total Rg total_rg25.43
Total atoms total_atoms3784
Residues n_residues492
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 dmax88.7
Rg (real space) rg_real25.52
Rg uncertainty (real space) rg_real_error0.75
I(0) (real space) i0_real4.9990e+07
I(0) uncertainty (real space) i0_real_error7.7620e+05
Rg (reciprocal space) rg_reciprocal25.50
I(0) (reciprocal space) i0_reciprocal49990000.0000
Solution quality estimate total_estimate0.7041
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2
Skewness Skewness skewness0.459
Kurtosis Kurtosis kurtosis-0.135
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha20320000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.756; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 0.955; Smooth: 0.981

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd3u4la1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.0 — automated matches
Domain ID domain_idd3u4la2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.1 — Actin-like ATPase domain
Family Family familyc.55.1.1 — Actin/HSP70
Domain ID domain_idd3u4lp_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.110 — Profilin-like
Superfamily Superfamily superfamilyd.110.1 — Profilin (actin-binding protein)
Family Family familyd.110.1.1 — Profilin (actin-binding protein)

CATH v4.4 (4 domains)

Domain ID domain_id3u4lA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3u4lA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily40 — ATPase, nucleotide binding domain
Domain ID domain_id3u4lA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology640 — Actin; Chain A, domain 4
Homologous superfamily homologous superfamily10 — ATPase, substrate binding domain, subdomain 4
Domain ID domain_id3u4lP00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily30 — Dynein light chain 2a, cytoplasmic

8. Citations (1)

9. Files and Curves (10)