2aef

Crystal Structures of the MthK RCK Domain in Ca2+ bound form

Method: X-RAY DIFFRACTION Dmax: 76.4 Å Quality: GOOD

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

Calcium-gated potassium channel mthK

Methanothermobacter thermautotrophicus

UniProt O27564

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 107–336 Chain B; UniProt 107–336 Fragment:isoform Soluble CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 4.5;293 K;PEG 4000, calcium chloride, Ammonium formate, sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 1.70 Å R-free 0.268

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.

47 other PDB entries and 76 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MTHK_METTH
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–230; UniProt 107–336 Author chain B; PDBConstruct 1–230; UniProt 107–336

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 2aef

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2aef
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2aef
Deposition date deposition_date2005-07-22
Structure title titleCrystal Structures of the MthK RCK Domain in Ca2+ bound form
Keywords keywordsRossmann fold, helix-turn-helix, Ca2+ binding, flexible interface, bilobed architecture, METAL TRANSPORT, membrane protein; METAL TRANSPORT, membrane protein
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.91
Radius of gyration Rg (electron density) rg_electron22.86
Forward intensity I(0) i038579200.00
Molecular weight molecular_weight47532.0 kDa
Excluded volume excluded_volume59428 ų
Envelope volume envelope_volume70245 ų
Hydration-shell volume shell_volume25660 ų
Envelope diameter envelope_diameter81.3
Shell Rg shell_rg29.66
Envelope Rg envelope_rg22.95
Shape Rg shape_rg22.89
Total Rg total_rg23.57
Total atoms total_atoms3336
Residues n_residues440
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 dmax76.4
Rg (real space) rg_real23.80
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real3.8580e+07
I(0) uncertainty (real space) i0_real_error5.2810e+05
Rg (reciprocal space) rg_reciprocal23.83
I(0) (reciprocal space) i0_reciprocal38580000.0000
Solution quality estimate total_estimate0.8989
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.5
Skewness Skewness skewness0.176
Kurtosis Kurtosis kurtosis-0.522
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12610000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd2aefa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.9 — Potassium channel NAD-binding domain
Domain ID domain_idd2aefa2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.286 — TrkA C-terminal domain-like
Superfamily Superfamily superfamilyd.286.1 — TrkA C-terminal domain-like
Family Family familyd.286.1.1 — TrkA C-terminal domain-like
Domain ID domain_idd2aefa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2aefb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.9 — Potassium channel NAD-binding domain
Domain ID domain_idd2aefb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.286 — TrkA C-terminal domain-like
Superfamily Superfamily superfamilyd.286.1 — TrkA C-terminal domain-like
Family Family familyd.286.1.1 — TrkA C-terminal domain-like

CATH v4.4 (6 domains)

Domain ID domain_id2aefA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2aefA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily870 — Voltage-gated potassium channel
Domain ID domain_id2aefA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1450 — Regulator of K+ conductance, C-terminal domain
Domain ID domain_id2aefB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id2aefB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily870 — Voltage-gated potassium channel
Domain ID domain_id2aefB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily1450 — Regulator of K+ conductance, C-terminal domain

8. Citations (1)

9. Files and Curves (10)