4pdr

Crystal Structure of a K+ selective NaK mutant in Barium and Sodium

Method: X-RAY DIFFRACTION Dmax: 108.8 Å Quality: REASONABLE

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

Potassium channel protein

Bacillus cereus

UniProt Q81HW2

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 20–110 Fragment:UNP residues 20-110 Mutation:D66Y,N68D BA BARIUM ION × 12 NA SODIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;293 K;65%MPD, 100mM KCl, 100mM MES, 4mM n-Decyl-beta-D-Maltoside Resolution 1.85 Å R-free 0.227
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 20–110 Fragment:UNP residues 20-110 Mutation:D66Y,N68D BA BARIUM ION × 12 NA SODIUM ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 12 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6;293 K;65%MPD, 100mM KCl, 100mM MES, 4mM n-Decyl-beta-D-Maltoside Resolution 1.85 Å R-free 0.227

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.

44 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q81HW2_BACCR
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–93; UniProt 20–110 Author chain B; PDBConstruct 3–93; UniProt 20–110

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 4pdr

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4pdr
Deposition date deposition_date2014-04-21
Structure title titleCrystal Structure of a K+ selective NaK mutant in Barium and Sodium
Keywords keywords;Bacillus cereus, Binding Sites, Electrophysiology, Ions, Potassium, Potassium Channels, Sodium, rubidium, blockage, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.80
Radius of gyration Rg (electron density) rg_electron28.98
Forward intensity I(0) i06447920.00
Molecular weight molecular_weight22218.0 kDa
Excluded volume excluded_volume28807 ų
Envelope volume envelope_volume39612 ų
Hydration-shell volume shell_volume13039 ų
Envelope diameter envelope_diameter113.8
Shell Rg shell_rg31.12
Envelope Rg envelope_rg30.02
Shape Rg shape_rg29.11
Total Rg total_rg28.76
Total atoms total_atoms1525
Residues n_residues189
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 dmax108.8
Rg (real space) rg_real28.62
Rg uncertainty (real space) rg_real_error1.58
I(0) (real space) i0_real6.4480e+06
I(0) uncertainty (real space) i0_real_error1.1070e+05
Rg (reciprocal space) rg_reciprocal28.37
I(0) (reciprocal space) i0_reciprocal6447000.0000
Solution quality estimate total_estimate0.6925
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.0
Skewness Skewness skewness0.714
Kurtosis Kurtosis kurtosis-0.092
Angular range angular_range— – 0.2850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha319100.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.316; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.064; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4pdrA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70
Domain ID domain_id4pdrB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily70

8. Citations (1)

9. Files and Curves (10)