4l76

Ca2+-bound E212Q mutant MthK RCK domain

Method: X-RAY DIFFRACTION Dmax: 119.1 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:RCK domain (UNP residues 107-336) Mutation:E212Q CA CALCIUM ION × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;295 K;8% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 0.2 M calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.99 Å R-free 0.263
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 107–336 Chain D; UniProt 107–336 Fragment:RCK domain (UNP residues 107-336) Mutation:E212Q CA CALCIUM ION × 5 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;295 K;8% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 0.2 M calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.99 Å R-free 0.263
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 107–336 Chain F; UniProt 107–336 Fragment:RCK domain (UNP residues 107-336) Mutation:E212Q CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.8;295 K;8% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 0.2 M calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.99 Å R-free 0.263

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 74 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 Author chain C; PDBConstruct 1–230; UniProt 107–336 Author chain D; PDBConstruct 1–230; UniProt 107–336 Author chain E; PDBConstruct 1–230; UniProt 107–336 Author chain F; 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 4l76

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4l76
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4l76
Deposition date deposition_date2013-06-13
Structure title titleCa2+-bound E212Q mutant MthK RCK domain
Keywords keywordsRossmann Fold, regulatory domain, calcium binding, membrane-associated, METAL TRANSPORT; METAL TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.93
Radius of gyration Rg (electron density) rg_electron36.34
Forward intensity I(0) i0332771000.00
Molecular weight molecular_weight145800.0 kDa
Excluded volume excluded_volume181880 ų
Envelope volume envelope_volume238690 ų
Hydration-shell volume shell_volume54734 ų
Envelope diameter envelope_diameter118.9
Shell Rg shell_rg42.77
Envelope Rg envelope_rg35.86
Shape Rg shape_rg36.36
Total Rg total_rg36.68
Total atoms total_atoms10217
Residues n_residues1340
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 dmax119.1
Rg (real space) rg_real36.91
Rg uncertainty (real space) rg_real_error0.96
I(0) (real space) i0_real3.3280e+08
I(0) uncertainty (real space) i0_real_error5.4580e+06
Rg (reciprocal space) rg_reciprocal36.92
I(0) (reciprocal space) i0_reciprocal332800000.0000
Solution quality estimate total_estimate0.8835
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.6
Skewness Skewness skewness0.347
Kurtosis Kurtosis kurtosis-0.431
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha56760000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.919

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 35 domains

SCOP 2.08 (17 domains)

Domain ID domain_idd4l76a1
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_idd4l76a2
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.286.1.0 — automated matches
Domain ID domain_idd4l76a3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4l76b1
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_idd4l76b2
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.286.1.0 — automated matches
Domain ID domain_idd4l76b3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4l76c1
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_idd4l76c2
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.286.1.0 — automated matches
Domain ID domain_idd4l76d1
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_idd4l76d2
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.286.1.0 — automated matches
Domain ID domain_idd4l76d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4l76e1
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_idd4l76e2
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.286.1.0 — automated matches
Domain ID domain_idd4l76e3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd4l76f1
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_idd4l76f2
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.286.1.0 — automated matches
Domain ID domain_idd4l76f3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (18 domains)

Domain ID domain_id4l76A01
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_id4l76A02
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_id4l76A03
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_id4l76B01
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_id4l76B02
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_id4l76B03
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_id4l76C01
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_id4l76C02
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_id4l76C03
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_id4l76D01
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_id4l76D02
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_id4l76D03
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_id4l76E01
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_id4l76E02
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_id4l76E03
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_id4l76F01
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_id4l76F02
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_id4l76F03
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)