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- PDB-3rbz: MthK channel, Ca2+-bound -

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Basic information

Entry
Database: PDB / ID: 3rbz
TitleMthK channel, Ca2+-bound
ComponentsCalcium-gated potassium channel mthK
KeywordsTRANSPORT PROTEIN / K+ channel / membrane protein / RCK domain / Ca2+ binding / Rossmann-fold
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Helix Hairpins - #70 ...Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsTaylor, A.B. / Parfenova, L.V. / Rothberg, B.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structures of multiple Ca2+-binding sites in a K+ channel RCK domain
Authors: Pau, V.P. / Smith, F.J. / Taylor, A.B. / Samakai, E. / Callaghan, M.M. / Abarca-Heidemann, K. / Parfenova, L.V. / Hart, P.J. / Rothberg, B.S.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
D: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,41216
Polymers150,9314
Non-polymers48112
Water0
1
A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
D: Calcium-gated potassium channel mthK
hetero molecules

A: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
C: Calcium-gated potassium channel mthK
D: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)302,82332
Polymers301,8628
Non-polymers96224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area42020 Å2
ΔGint-524 kcal/mol
Surface area88920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.558, 138.558, 371.620
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 116:336 ) and (not element H) and (not element D)
211chain B and (resseq 116:336 ) and (not element H) and (not element D)
311chain C and (resseq 116:336 ) and (not element H) and (not element D)
411chain D and (resseq 116:336 ) and (not element H) and (not element D)
112chain A and (resseq 27:86 ) and (not element H) and (not element D)
212chain B and (resseq 27:86 ) and (not element H) and (not element D)
312chain C and (resseq 27:86 ) and (not element H) and (not element D)
412chain D and (resseq 27:86 ) and (not element H) and (not element D)

NCS ensembles :
ID
1
2

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Components

#1: Protein
Calcium-gated potassium channel mthK


Mass: 37732.699 Da / Num. of mol.: 4 / Mutation: G85A, E92A, E96T, M107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: mthK, MTH_1520 / Plasmid: PQE80 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: O27564
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 26% PEG 350-MME, 0.2 M CaCl2, 0.1 M MES, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2005
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.5 Å / Num. obs: 28010 / % possible obs: 93.6 % / Redundancy: 11.3 % / Rsym value: 0.132
Reflection shellResolution: 3.39→3.39 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.421 / % possible all: 56.6

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LNQ, 3LDC, 2AEF

1lnq

3ldc

2aef


Resolution: 3.4→48.5 Å / SU ML: 0.49 / σ(F): 0 / Phase error: 26.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 1881 7.15 %RANDOM
Rwork0.2568 ---
obs0.259 26324 86.87 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.582 Å2 / ksol: 0.282 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.2894 Å2-0 Å2-0 Å2
2--15.2894 Å20 Å2
3----30.5788 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8141 0 12 0 8153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0128243
X-RAY DIFFRACTIONf_angle_d1.27211200
X-RAY DIFFRACTIONf_dihedral_angle_d17.0482891
X-RAY DIFFRACTIONf_chiral_restr0.0761337
X-RAY DIFFRACTIONf_plane_restr0.0041488
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1685X-RAY DIFFRACTIONPOSITIONAL
12B1685X-RAY DIFFRACTIONPOSITIONAL0.052
13C1681X-RAY DIFFRACTIONPOSITIONAL0.064
14D1675X-RAY DIFFRACTIONPOSITIONAL0.075
21A324X-RAY DIFFRACTIONPOSITIONAL
22B324X-RAY DIFFRACTIONPOSITIONAL0.015
23C313X-RAY DIFFRACTIONPOSITIONAL0.017
24D314X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.387-3.50810.463880.36361187X-RAY DIFFRACTION43
3.5081-3.64850.37421420.35231787X-RAY DIFFRACTION65
3.6485-3.81450.3441820.31142325X-RAY DIFFRACTION85
3.8145-4.01550.29311950.25792509X-RAY DIFFRACTION91
4.0155-4.26690.25911950.22372563X-RAY DIFFRACTION92
4.2669-4.59610.21092040.1882698X-RAY DIFFRACTION97
4.5961-5.05820.22282060.20172707X-RAY DIFFRACTION97
5.0582-5.78910.29112150.24472784X-RAY DIFFRACTION98
5.7891-7.28970.24282190.25222831X-RAY DIFFRACTION98
7.2897-48.55420.32822350.28173052X-RAY DIFFRACTION99

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