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- PDB-4l75: Ca2+-bound D184N mutant MthK RCK domain at 2.4 Angstrom -

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Basic information

Entry
Database: PDB / ID: 4l75
TitleCa2+-bound D184N mutant MthK RCK domain at 2.4 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: 2.393 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 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_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_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
C: Calcium-gated potassium channel MthK
D: Calcium-gated potassium channel MthK
E: Calcium-gated potassium channel MthK
F: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,56012
Polymers161,3206
Non-polymers2406
Water4,270237
1
A: Calcium-gated potassium channel MthK
B: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8534
Polymers53,7732
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-64 kcal/mol
Surface area20130 Å2
MethodPISA
2
C: Calcium-gated potassium channel MthK
D: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8534
Polymers53,7732
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-64 kcal/mol
Surface area19340 Å2
MethodPISA
3
E: Calcium-gated potassium channel MthK
F: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8534
Polymers53,7732
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-64 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.228, 119.228, 353.958
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
Calcium-gated potassium channel MthK


Mass: 26886.609 Da / Num. of mol.: 6 / Fragment: RCK domain (UNP residues 107-336) / Mutation: D184N
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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 7% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 0.3 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: Oct 5, 2011
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: 2.393→45 Å / Num. all: 59525 / Num. obs: 59525 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 16.6 % / Rmerge(I) obs: 0.084 / Χ2: 0.861 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.393-2.4910.358160.4591100
2.49-2.5914.158210.47211000.846
2.59-2.715.858610.63511000.646
2.7-2.8519.258690.52511000.381
2.85-3.0218.558530.58111000.254
3.02-3.2618.359210.72911000.154
3.26-3.5817.359381.04411000.106
3.58-4.116.760071.348199.90.077
4.1-5.1718.360401.341199.60.059
5.17-4517.663991.1971990.044

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2aef


Resolution: 2.393→44.593 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / σ(F): 1.36 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 2020 3.4 %THIN-RESOLUTION SHELLS
Rwork0.1958 ---
obs0.1975 59397 99.55 %-
all-59397 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.76 Å2 / Biso mean: 72.7784 Å2 / Biso min: 32.38 Å2
Refinement stepCycle: LAST / Resolution: 2.393→44.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10337 0 6 237 10580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710464
X-RAY DIFFRACTIONf_angle_d1.01614137
X-RAY DIFFRACTIONf_chiral_restr0.0451649
X-RAY DIFFRACTIONf_plane_restr0.0051861
X-RAY DIFFRACTIONf_dihedral_angle_d13.3723973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.393-2.45290.39381010.28433904400596
2.4529-2.51920.31322020.263539744176100
2.5192-2.59330.3021010.244741024203100
2.5933-2.6770.28262020.250339594161100
2.677-2.77270.27551010.234741054206100
2.7727-2.88360.2761010.249140684169100
2.8836-3.01490.31082020.253240224224100
3.0149-3.17380.28071010.230941114212100
3.1738-3.37260.27062020.228340244226100
3.3726-3.63280.2491010.209841764277100
3.6328-3.99820.23122020.175940744276100
3.9982-4.57630.18551010.149542094310100
4.5763-5.76370.20441010.165342734374100
5.7637-44.60040.23072020.18154376457898
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)
18.9281.3403-0.90064.09362.34755.3332-0.09280.2024-0.1788-0.0748-0.0435-0.28510.42670.37490.14430.64490.11450.1260.44390.10320.42734.1348-35.8566-41.6902
20.3615-0.3532-1.42757.74024.53276.81450.0213-0.080.0354-0.2391-0.33190.6724-0.1156-0.31260.28040.34680.02080.05630.4923-0.04130.447520.0393-21.2978-34.8408
37.08620.94020.47565.5281-0.48828.65970.1493-0.19140.14470.5133-0.2571-0.24520.54660.19250.10840.51060.03820.04550.36270.01430.43627.9274-26.9403-11.8925
48.58421.96052.28632.93420.07775.77720.06470.154-0.1059-0.0804-0.16880.13670.04030.00260.10220.44930.11280.05090.3455-0.02050.395320.1778-6.4632-46.1527
51.6836-1.5142-1.49626.10112.94715.3362-0.0958-0.1927-0.02030.218-0.08220.48570.0973-0.22110.190.3058-0.01050.02460.40680.03680.403120.2978-12.551-18.7135
67.18982.63120.5587.62251.69765.1665-0.1015-0.20260.8048-0.1318-0.16290.1027-0.61340.08420.26330.54270.0163-0.12910.3816-0.09510.652-15.2896-22.497-15.5037
78.5048-3.5734-3.45821.64461.23554.6268-0.30190.3942-0.2137-0.34750.0715-0.04380.11870.05930.25620.661-0.17240.01610.4308-0.11390.5302-8.2247-41.2054-23.4604
87.2868-1.1506-1.39353.6988-1.25844.62540.57131.9810.8043-0.7181-0.3466-0.6274-0.4901-0.6293-0.13810.83030.04170.05960.88830.21510.6471-9.7855-30.9322-45.5424
98.88742.06610.85284.7144-1.67854.5192-0.1814-0.1078-0.24370.18730.21840.01070.24820.3444-0.050.62820.08380.18560.4232-0.04470.37944.0113-50.0473-11.092
105.1406-1.27263.58780.6011-0.17025.6122-0.44420.33460.3601-0.12810.15360.0481-0.55070.45280.30440.5646-0.1820.02620.42330.0540.4989-1.8956-34.0101-24.1346
116.9779-0.68310.33076.8311.61486.705-0.2460.8767-0.4417-1.05320.32790.3938-0.10760.2026-0.09260.7549-0.15720.01050.5411-0.06540.51092.7842-48.3236-43.7067
126.13271.3369-0.31064.7828-0.41453.3614-0.0615-0.4701-0.47890.0778-0.4097-0.18270.85760.61280.40.83610.24430.31420.67170.27660.82461.273-15.8171-11.7321
133.581-0.53380.96020.7858-0.62053.6046-0.4353-0.0571-0.1289-0.0475-0.0859-0.19970.14440.62960.52270.55120.02740.14520.6060.19680.60159.7439-0.8211-22.6023
147.4564-0.99082.8774.31472.08976.7115-0.08130.6687-0.4493-0.26460.1079-0.10370.27470.723-0.01550.51030.00940.18480.5012-0.03780.584959.8065-11.3601-44.3714
153.073.0616-0.50066.35232.29316.1159-0.09580.07890.07780.1836-0.0059-0.4877-0.43140.52190.15590.51160.0645-0.11420.41480.06010.564244.487514.1613-14.0766
169.4396-3.8808-4.36782.70151.28964.9067-0.62420.1052-0.5957-0.0157-0.0083-0.12520.49980.17480.60170.4482-0.04110.08550.39720.00190.47747.5719-2.6185-23.348
178.1325-3.17913.40974.6326-5.83638.5578-0.6811-0.47511.31120.53520.052-0.5814-1.07520.92470.58430.5507-0.08190.03080.567-0.02510.704656.50387.8693-36.2329
187.5663-0.53031.95688.4121-1.54759.42320.11320.85730.4495-0.3124-0.39-0.0416-0.1987-0.02870.24720.36710.05770.05680.46170.03150.384847.18366.0977-47.6803
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 112 through 213 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 214 through 254 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 255 through 339 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 115 through 230 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 231 through 338 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 116 through 213 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 214 through 255 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 256 through 336 )C0
9X-RAY DIFFRACTION9chain 'D' and (resid 116 through 213 )D0
10X-RAY DIFFRACTION10chain 'D' and (resid 214 through 255 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 256 through 338 )D0
12X-RAY DIFFRACTION12chain 'E' and (resid 116 through 199 )E0
13X-RAY DIFFRACTION13chain 'E' and (resid 200 through 255 )E0
14X-RAY DIFFRACTION14chain 'E' and (resid 256 through 336 )E0
15X-RAY DIFFRACTION15chain 'F' and (resid 116 through 201 )F0
16X-RAY DIFFRACTION16chain 'F' and (resid 202 through 255 )F0
17X-RAY DIFFRACTION17chain 'F' and (resid 256 through 268 )F0
18X-RAY DIFFRACTION18chain 'F' and (resid 269 through 338 )F0

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