3ifx

Crystal structure of the Spin-labeled KcsA mutant V48R1

Dmax: 67.5 Å Quality: EXCELLENT

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

Voltage-gated potassium channel

Streptomyces lividans

UniProt P0A334

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 1–123 Chain B; UniProt 1–123 Chain C; UniProt 1–123 Chain D; UniProt 1–123 Fragment:Pore domain: UNP residues 1-124 Mutation:V48C K POTASSIUM ION × 2 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 4 TBA TETRABUTYLAMMONIUM ION × 1 Experimental method not declared X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;200 mM CaCl2, 150 mM KCl, 100 mM HEPES, 19-49% PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.56 Å R-free 0.302
2 Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric(8) Consistent with protein copy count Chain A; UniProt 1–123 Chain B; UniProt 1–123 Chain C; UniProt 1–123 Chain D; UniProt 1–123 Fragment:Pore domain: UNP residues 1-124 Mutation:V48C K POTASSIUM ION × 4 MTN S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate × 8 TBA TETRABUTYLAMMONIUM ION × 2 Experimental method not declared X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;200 mM CaCl2, 150 mM KCl, 100 mM HEPES, 19-49% PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.56 Å R-free 0.302

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.

86 other PDB entries and 95 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KCSA_STRLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–123; UniProt 1–123 Author chain B; PDBConstruct 1–123; UniProt 1–123 Author chain C; PDBConstruct 1–123; UniProt 1–123 Author chain D; PDBConstruct 1–123; UniProt 1–123

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 3ifx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3ifx
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3ifx
Deposition date deposition_date2009-07-26
Structure title titleCrystal structure of the Spin-labeled KcsA mutant V48R1
Keywords keywords;potassium channel, spin-labeled protein, membrane protein, Cell membrane, Ion transport, Ionic channel, Membrane, Transmembrane, Transport, Voltage-gated channel ;; MEMBRANE PROTEIN

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

Radius of gyration Rg (Guinier) rg_guinier21.78
Radius of gyration Rg (electron density) rg_electron20.62
Forward intensity I(0) i021791800.00
Molecular weight molecular_weight39518.0 kDa
Excluded volume excluded_volume51168 ų
Envelope volume envelope_volume59031 ų
Hydration-shell volume shell_volume23535 ų
Envelope diameter envelope_diameter66.7
Shell Rg shell_rg27.62
Envelope Rg envelope_rg20.88
Shape Rg shape_rg20.63
Total Rg total_rg21.61
Total atoms total_atoms2792
Residues n_residues388
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 dmax67.5
Rg (real space) rg_real21.64
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real2.1790e+07
I(0) uncertainty (real space) i0_real_error2.7530e+05
Rg (reciprocal space) rg_reciprocal21.67
I(0) (reciprocal space) i0_reciprocal21790000.0000
Solution quality estimate total_estimate0.9081
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.2
Skewness Skewness skewness0.133
Kurtosis Kurtosis kurtosis-0.485
Angular range angular_range— – 0.3650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3666000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3ifxA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id3ifxB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id3ifxC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id3ifxD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70

8. Citations (1)

9. Files and Curves (10)