3rbx

MthK RCK domain D184N mutant, Ca2+-bound

Method: X-RAY DIFFRACTION Dmax: 118.5 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:unp residues 107-336 Mutation:D184N CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;295 K;20% PEG 3350, 0.1 M CaCl2, 0.1 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 5.7 Resolution 2.80 Å R-free 0.274
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:unp residues 107-336 Mutation:D184N CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;295 K;20% PEG 3350, 0.1 M CaCl2, 0.1 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 5.7 Resolution 2.80 Å R-free 0.274
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:unp residues 107-336 Mutation:D184N CA CALCIUM ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.7;295 K;20% PEG 3350, 0.1 M CaCl2, 0.1 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K, pH 5.7 Resolution 2.80 Å R-free 0.274

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 3rbx

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3rbx
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3rbx
Deposition date deposition_date2011-03-30
Structure title titleMthK RCK domain D184N mutant, Ca2+-bound
Keywords keywordsK+ channel, RCK domain, Rossman-fold, Ca2+ binding domain, 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_guinier36.72
Radius of gyration Rg (electron density) rg_electron36.19
Forward intensity I(0) i0321251000.00
Molecular weight molecular_weight143450.0 kDa
Excluded volume excluded_volume178930 ų
Envelope volume envelope_volume229870 ų
Hydration-shell volume shell_volume53226 ų
Envelope diameter envelope_diameter119.8
Shell Rg shell_rg42.53
Envelope Rg envelope_rg35.68
Shape Rg shape_rg36.21
Total Rg total_rg36.51
Total atoms total_atoms10055
Residues n_residues1320
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 dmax118.5
Rg (real space) rg_real36.71
Rg uncertainty (real space) rg_real_error0.90
I(0) (real space) i0_real3.2130e+08
I(0) uncertainty (real space) i0_real_error4.6260e+06
Rg (reciprocal space) rg_reciprocal36.72
I(0) (reciprocal space) i0_reciprocal321300000.0000
Solution quality estimate total_estimate0.8824
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.3
Skewness Skewness skewness0.355
Kurtosis Kurtosis kurtosis-0.429
Angular range angular_range— – 0.2150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha46860000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.853; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.909

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd3rbxa1
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_idd3rbxa2
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_idd3rbxb1
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_idd3rbxb2
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_idd3rbxc1
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_idd3rbxc2
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_idd3rbxd1
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_idd3rbxd2
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_idd3rbxe1
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_idd3rbxe2
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_idd3rbxf1
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_idd3rbxf2
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

CATH v4.4 (18 domains)

Domain ID domain_id3rbxA01
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_id3rbxA02
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_id3rbxA03
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_id3rbxB01
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_id3rbxB02
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_id3rbxB03
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_id3rbxC01
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_id3rbxC02
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_id3rbxC03
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_id3rbxD01
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_id3rbxD02
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_id3rbxD03
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_id3rbxE01
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_id3rbxE02
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_id3rbxE03
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_id3rbxF01
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_id3rbxF02
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_id3rbxF03
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)