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- PDB-6u9z: Wild-type MthK pore in 6 mM K+ -

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Basic information

Entry
Database: PDB / ID: 6u9z
TitleWild-type MthK pore in 6 mM K+
ComponentsCalcium-gated potassium channel MthK
KeywordsTRANSPORT PROTEIN / Potassium ion channel MthK
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
: / 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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / : / Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.954 Å
AuthorsPosson, D.J. / Nimigean, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM088352 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM087865 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Selectivity filter ion binding affinity determines inactivation in a potassium channel.
Authors: Boiteux, C. / Posson, D.J. / Allen, T.W. / Nimigean, C.M.
History
DepositionSep 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2937
Polymers8,9801
Non-polymers3146
Water54030
1
A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules

A: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,17328
Polymers35,9184
Non-polymers1,25524
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area6530 Å2
ΔGint-62 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.811, 63.811, 44.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-102-

K

31A-103-

K

41A-104-

K

51A-105-

K

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Components

#1: Protein Calcium-gated potassium channel MthK


Mass: 8979.500 Da / Num. of mol.: 1 / Fragment: UNP residues 18-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK, MTH_1520 / Production host: Escherichia coli (E. coli) / References: UniProt: O27564
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: protein (in 100 mM sodium chloride, 1 mM potassium chloride, 10 mM MOPS) + 3.5-4.0 M 1,6-hexanediol, 100 mM MES-NaOH, pH 6.75, 5 mM potassium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.009 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.954→44.05 Å / Num. obs: 6986 / % possible obs: 99.66 % / Redundancy: 24.7 % / Biso Wilson estimate: 27.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1864 / Rpim(I) all: 0.03809 / Rrim(I) all: 0.1903 / Net I/σ(I): 15.95
Reflection shellResolution: 1.954→2.024 Å / Redundancy: 22.5 % / Rmerge(I) obs: 2.1 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 660 / CC1/2: 0.751 / Rpim(I) all: 0.4475 / Rrim(I) all: 2.148 / % possible all: 97.05

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PHENIXphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LDC

3ldc


Resolution: 1.954→44.05 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7274
RfactorNum. reflection% reflection
Rfree0.2263 691 10.04 %
Rwork0.2046 --
obs0.2067 6982 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.49 Å2
Refinement stepCycle: LAST / Resolution: 1.954→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms637 0 13 30 680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024687
X-RAY DIFFRACTIONf_angle_d0.4328946
X-RAY DIFFRACTIONf_chiral_restr0.0351119
X-RAY DIFFRACTIONf_plane_restr0.0026111
X-RAY DIFFRACTIONf_dihedral_angle_d2.0876501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.954-2.0240.3087640.3005660X-RAY DIFFRACTION97.05
2.03-2.120.26771580.2651255X-RAY DIFFRACTION99.86
2.12-2.240.2711490.23351235X-RAY DIFFRACTION100
2.24-2.380.23361680.21591234X-RAY DIFFRACTION99.93
2.38-2.560.23051340.18391264X-RAY DIFFRACTION100
2.56-2.820.21211310.16891273X-RAY DIFFRACTION100
2.82-3.230.18151170.17941290X-RAY DIFFRACTION100
3.23-4.060.19211440.19481260X-RAY DIFFRACTION100
4.06-44.050.24571320.20951276X-RAY DIFFRACTION99.93
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)
15.862514411794.084594034272.583145638127.790566596391.957738099954.044731136010.0275549515294-0.659044657366-0.09185470999640.8227029609270.1591497797260.3738248348630.0143404869463-0.0923600266641-0.2039996877060.2924813378310.09828399227740.02183152281560.4006458874880.0004750939226580.2152162341848.4270111982615.22169728056.6584970487
23.24254817966-1.086191209370.4103721329973.06175414004-1.250634269052.673932743420.1136701487260.137652208368-0.27610276923-0.07987342991660.00198568282278-0.002569309160370.3278187894810.041582566437-0.1096559605910.278199486207-0.00334120548157-0.02601901874380.216406564601-0.005925540059550.1712556938012.0001002613418.6143247287-8.96483348513
36.76760451085-0.08661443071691.801716594453.54237726965-0.1653307247557.17790096951-0.195292226939-1.45900257460.9957166778031.56618785306-0.214307155601-0.647187959734-0.05633993186181.23740697780.4088138632050.8730111911950.0245457093596-0.2301044149940.683754704494-0.1494308677780.54518337814812.888954742526.84290297619.99363076502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 18:31)
2X-RAY DIFFRACTION2(chain A and resid 32:90)
3X-RAY DIFFRACTION3(chain A and resid 91:99)

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