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- PDB-6oly: Full-length MthK channel at 3.1 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6oly
TitleFull-length MthK channel at 3.1 angstrom resolution
ComponentsCalcium-gated potassium channel MthK
KeywordsMEMBRANE PROTEIN / potassium channel / calcium-binding / RCK domain / 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
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. / Potassium channel domain / Ion channel / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.112 Å
AuthorsRothberg, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1243803 United States
CitationJournal: Nat Commun / Year: 2019
Title: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling.
Authors: Kopec, W. / Rothberg, B.S. / de Groot, B.L.
History
DepositionApr 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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.ptnr2_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)155,59216
Polymers155,1114
Non-polymers48112
Water32418
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)311,18432
Polymers310,2228
Non-polymers96224
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area43260 Å2
ΔGint-550 kcal/mol
Surface area103300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.456, 137.456, 373.026
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21D-501-

HOH

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Components

#1: Protein
Calcium-gated potassium channel MthK


Mass: 38777.723 Da / Num. of mol.: 4 / Mutation: M107I
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.28 Å3/Da / Density % sol: 62.49 %
Description: hexagonal rod with ends tapered to a point ("almond-shape")
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 28% PEG350-MME, 0.1M MES pH 6.5, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.112→39.702 Å / Num. obs: 37785 / % possible obs: 98.24 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.038 / Net I/σ(I): 25.4
Reflection shellResolution: 3.112→3.223 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3251 / CC1/2: 0.489

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Processing

Software
NameVersionClassification
PHENIX(dev_3374: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RBZ
Resolution: 3.112→39.702 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.15
RfactorNum. reflection% reflection
Rfree0.2746 1899 5.04 %
Rwork0.2356 --
obs0.2376 37708 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.112→39.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8745 0 12 18 8775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068851
X-RAY DIFFRACTIONf_angle_d0.90412050
X-RAY DIFFRACTIONf_dihedral_angle_d2.6695333
X-RAY DIFFRACTIONf_chiral_restr0.0581452
X-RAY DIFFRACTIONf_plane_restr0.0061610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1119-3.18970.5063950.42512133X-RAY DIFFRACTION83
3.1897-3.27590.45571900.40512404X-RAY DIFFRACTION96
3.2759-3.37220.3765950.37622534X-RAY DIFFRACTION99
3.3722-3.4810.4637940.33022575X-RAY DIFFRACTION99
3.481-3.60530.36411900.31072502X-RAY DIFFRACTION100
3.6053-3.74960.344950.28132587X-RAY DIFFRACTION100
3.7496-3.92010.30211900.24842513X-RAY DIFFRACTION100
3.9201-4.12660.3038950.21892593X-RAY DIFFRACTION100
4.1266-4.38480.22231900.18372533X-RAY DIFFRACTION100
4.3848-4.72290.2159950.17672649X-RAY DIFFRACTION100
4.7229-5.19720.2287950.1862647X-RAY DIFFRACTION100
5.1972-5.94710.27771900.2412586X-RAY DIFFRACTION100
5.9471-7.48450.2627950.24842727X-RAY DIFFRACTION100
7.4845-39.70530.2161900.19232826X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.72733.988-1.25062.3907-0.26669.2951-0.92010.3794-0.68590.6228-1.13260.23890.16730.81262.04241.49360.24710.2821.46170.59363.5421-12.16970.010112.8318
27.7527-1.14021.29489.5093-2.55415.6615-0.2032-0.1886-0.11040.80320.0502-1.0325-0.29120.97070.1940.8158-0.1921-0.05931.2343-0.05740.4208-51.684326.62884.941
33.3987-0.11571.56096.6407-1.35042.7025-0.5937-0.28950.88230.72840.5599-0.4792-0.7720.5666-0.14890.9924-0.17830.13911.0301-0.09930.6944-60.187749.8265-8.448
46.16014.2943-2.21053.95753.7955.03450.7381.26450.4522-0.83050.1251-0.16450.5051-0.2261-1.01171.63540.0451-0.3532.1340.02872.0194-13.380913.1733-0.4577
56.07040.24091.78078.33330.60976.0861-0.2025-0.1471-0.0054-0.31060.207-1.28-0.57020.8929-0.030.8071-0.06030.13670.9184-0.11520.5309-51.5065.4776-26.4404
66.66981.5057-2.35555.0170.30849.9569-0.33061.43030.1634-1.84850.4237-0.80680.5962-0.0533-0.05811.583-0.15440.23871.0462-0.15260.6064-58.575-8.2957-49.8547
75.58961.1011-2.05444.03131.8210.67670.4424-0.4957-0.49660.5219-0.21240.38251.13150.8622-0.22491.97410.1061-0.12552.59850.67032.3173-112.6112.7333-1.8029
87.30970.73520.52187.7392-0.78478.2441-0.1919-0.14870.05470.61790.14740.4208-0.7012-0.5850.08330.79180.1232-0.04950.73860.0440.3205-73.85917.163321.2025
94.323-5.0803-5.93845.51216.76816.4131-0.7479-1.09250.43431.19531.1275-0.40450.4161.243-0.181.54090.0882-0.13781.243-0.07610.5325-66.735816.564248.1476
102.72192.9156-1.26684.3941.21738.51561.11930.38-0.019-1.8154-1.0834-0.1508-1.2446-0.01730.11652.14160.2549-0.42781.3712-0.24963.4526-114.17051.948712.6426
117.5771-0.27152.60686.51492.31869.0712-0.21220.76990.1331-0.16970.15770.3441-0.6223-0.28740.05730.69090.21130.0310.7136-0.02340.4009-74.6254-20.415117.0254
123.84483.1809-2.69268.9399-3.73523.1868-0.2094-0.2501-0.26830.28610.08510.07450.27560.00190.13620.9391-0.0368-0.12320.7372-0.14380.4136-68.5071-47.721315.8723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 108 )
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 230 )
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 336 )
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 108 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 230 )
6X-RAY DIFFRACTION6chain 'B' and (resid 231 through 336 )
7X-RAY DIFFRACTION7chain 'C' and (resid 22 through 110 )
8X-RAY DIFFRACTION8chain 'C' and (resid 111 through 230 )
9X-RAY DIFFRACTION9chain 'C' and (resid 231 through 339 )
10X-RAY DIFFRACTION10chain 'D' and (resid 25 through 109 )
11X-RAY DIFFRACTION11chain 'D' and (resid 110 through 230 )
12X-RAY DIFFRACTION12chain 'D' and (resid 231 through 336 )

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