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- PDB-4l73: Ca2+-bound MthK RCK domain at 2.5 Angstrom -

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Basic information

Entry
Database: PDB / ID: 4l73
TitleCa2+-bound MthK RCK domain at 2.5 Angstrom
ComponentsCalcium-gated potassium channel MthK
KeywordsMETAL TRANSPORT / Rossmann Fold / regulatory domain / calcium binding / membrane-associated
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. ...Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / : / TrkA-N domain / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / 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 / molecular replacement / Resolution: 2.5 Å
AuthorsSmith, F.J. / Rothberg, B.S.
CitationJournal: Nat Commun / Year: 2013
Title: Structural basis of allosteric interactions among Ca(2+)-binding sites in a K(+) channel RCK domain.
Authors: Smith, F.J. / Pau, V.P. / Cingolani, G. / Rothberg, B.S.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Sep 20, 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,19516
Polymers53,7752
Non-polymers42014
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint-38 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.960, 67.960, 159.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-403-

CL

21B-519-

HOH

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Components

#1: Protein Calcium-gated potassium channel MthK


Mass: 26887.594 Da / Num. of mol.: 2 / Fragment: RCK domain (UNP residues 107-336)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 12% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 1 M calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→39.506 Å / Num. all: 14924 / Num. obs: 14924 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5 % / Rsym value: 0.121
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.403 / % possible all: 89.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AEF

2aef


Resolution: 2.5→39.506 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 743 5 %RANDOM
Rwork0.1783 ---
obs0.1808 14863 96.24 %-
all-14924 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.32 Å2 / Biso mean: 54.3949 Å2 / Biso min: 26.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 14 95 3539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083472
X-RAY DIFFRACTIONf_angle_d1.0844690
X-RAY DIFFRACTIONf_chiral_restr0.068548
X-RAY DIFFRACTIONf_plane_restr0.005616
X-RAY DIFFRACTIONf_dihedral_angle_d13.9861316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.6930.34161320.25052575270790
2.693-2.96390.27951520.22952860301299
2.9639-3.39260.27181500.2012845299598
3.3926-4.27350.2031470.15472870301798
4.2735-39.51080.17851620.15352970313296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4195-1.45451.7577.7425-1.21015.5816-0.10350.5481-0.301-0.14330.09420.1937-0.0705-0.43050.01830.3608-0.08490.04820.5211-0.10180.416812.1245.81412.3952
26.09771.8737-5.52492.5339-1.26557.49090.2074-0.01520.37540.02640.0590.1664-0.2779-0.1478-0.14930.3481-0.0117-0.02080.3715-0.04110.429724.71619.588327.8733
36.8360.9887-3.98713.8946-0.31636.0945-0.05620.20890.1586-0.18750.045-0.3694-0.04810.2727-0.0280.3993-0.02230.00590.42710.04350.457840.746221.668213.1598
44.0342-1.5704-0.03616.4522-2.19415.4084-0.027-0.2149-0.19180.17450.12940.20990.0469-0.0569-0.10.34150.00560.03450.38270.06710.377213.151111.370643.3118
54.99490.71850.93733.53312.71032.9808-0.07180.1886-0.77510.06850.1891-0.2460.06530.2421-0.08990.3682-0.02010.03450.36360.07580.391527.524113.391124.1976
67.01650.9470.65996.3021.31327.56710.1151-0.26270.49830.26460.0085-0.0654-0.03180.4007-0.12060.3342-0.02890.00030.3596-0.00480.540139.897627.40234.6057
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 115 through 230 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 231 through 268 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 269 through 338 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 115 through 230 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 231 through 268 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 269 through 336 )B0

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