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- PDB-4l76: Ca2+-bound E212Q mutant MthK RCK domain -

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Basic information

Entry
Database: PDB / ID: 4l76
TitleCa2+-bound E212Q mutant MthK RCK domain
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 / 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 / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / RCK N-terminal domain profile. ...Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / : / Regulator of K+ conductance, N-terminal / 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. / 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 / Resolution: 2.992 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_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
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)161,88721
Polymers161,3206
Non-polymers56715
Water181
1
A: Calcium-gated potassium channel MthK
B: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9577
Polymers53,7732
Non-polymers1835
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-99 kcal/mol
Surface area19660 Å2
MethodPISA
2
C: Calcium-gated potassium channel MthK
D: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9978
Polymers53,7732
Non-polymers2236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-113 kcal/mol
Surface area19260 Å2
MethodPISA
3
E: Calcium-gated potassium channel MthK
F: Calcium-gated potassium channel MthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9346
Polymers53,7732
Non-polymers1604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-89 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.884, 118.884, 356.052
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: 26886.607 Da / Num. of mol.: 6 / Fragment: RCK domain (UNP residues 107-336) / Mutation: E212Q
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.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 8% PEG4000, 1 M ammonium formate, 0.1 M sodium acetate, pH 4.8, 0.2 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 4, 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: 2.992→45 Å / Num. all: 30884 / Num. obs: 30884 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 16.7 % / Rmerge(I) obs: 0.167 / Χ2: 1.231 / Net I/σ(I): 4.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.992-3.1117.630030.5191100
3.11-3.2318.130500.5561100
3.23-3.3817.230100.6321100
3.38-3.5615.530521.24199.90.783
3.56-3.781530291.11199.70.504
3.78-4.0714.229331.427195.10.344
4.07-4.4816.930921.67911000.19
4.48-5.131831211.909199.90.152
5.13-6.4617.731841.51911000.14
6.46-4516.734101.673199.40.079

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Processing

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

2aef


Resolution: 2.992→44.563 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1997 6.5 %THIN-RESOLUTION SHELLS
Rwork0.2168 ---
obs0.2198 30704 98.8 %-
all-30704 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.78 Å2 / Biso mean: 104.692 Å2 / Biso min: 62.54 Å2
Refinement stepCycle: LAST / Resolution: 2.992→44.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10202 0 15 1 10218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210369
X-RAY DIFFRACTIONf_angle_d0.97914023
X-RAY DIFFRACTIONf_chiral_restr0.0411642
X-RAY DIFFRACTIONf_plane_restr0.0051839
X-RAY DIFFRACTIONf_dihedral_angle_d11.9423869
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 (%)
2.992-3.06640.4252990.31241964206395
3.0664-3.14930.32000.274219742174100
3.1493-3.2420.32121000.265720592159100
3.242-3.34660.36471990.26519662165100
3.3466-3.46610.39511000.308220652165100
3.4661-3.60480.25761000.237820962196100
3.6048-3.76880.3062000.2791933213399
3.7688-3.96740.3111000.23861969206993
3.9674-4.21580.2572000.211319792179100
4.2158-4.5410.21721000.166221102210100
4.541-4.99750.19451000.164321332233100
4.9975-5.71930.24882000.197320632263100
5.7193-7.20080.29761000.224621832283100
7.2008-44.56760.21761990.19282213241297
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)
14.7886-3.22170.44256.92944.55535.61330.53051.3033-2.2592-0.65970.34260.56660.60890.2074-1.17910.752-0.04680.12570.7826-0.01621.477436.8871-35.9363-37.5579
28.84581.6728-0.86788.74530.17395.16340.05320.35730.5285-0.2892-0.23460.22770.10680.05630.2140.78920.08360.10230.6651-0.01930.877230.6509-35.7765-42.1183
30.8101-0.47151.65512.0545-2.03838.23780.0934-0.0655-0.28830.0955-0.0443-0.03080.1725-0.0704-0.07430.7440.01520.08650.7952-0.0031.024726.2107-23.474-17.139
48.11160.650.55387.93680.76826.8742-0.18640.04730.062-0.2384-0.0060.2823-0.238-0.24890.25540.74380.07750.0110.67590.03230.964819.1644-6.6297-47.0869
50.5221-0.7999-1.17032.92990.4983.4616-0.1038-0.20460.17480.0564-0.00920.43130.2687-0.1830.12670.75370.01130.01290.86870.00431.150920.4423-12.5583-19.7792
67.6764.1035-0.34825.1755-0.26355.7689-0.1686-0.14950.08940.20150.1271-0.1031-0.5059-0.03110.00760.99550.095-0.13330.7992-0.0691.2858-16.3972-24.5238-16.3948
75.9783-4.68260.63674.1261-2.49758.23910.28721.15510.424-0.3273-0.5668-0.3513-0.1946-0.27040.24860.8792-0.07820.04930.92330.00521.1161-7.3073-34.1066-41.0538
85.47520.1073-0.24117.7114-2.2316.9731-0.1880.09540.04270.1316-0.05280.00280.36060.34020.26510.86570.04750.06990.81330.02031.06144.1885-48.2182-12.3628
94.2654-3.9759-2.15674.24642.90645.6771-0.09650.2582-0.5065-0.42140.03410.37180.235-0.10580.16010.9407-0.1263-0.08350.8698-0.07081.2074-0.9017-44.3508-39.8928
107.11641.42610.10633.3131-3.17536.3707-0.2263-0.0998-0.9244-0.0582-0.08910.27561.1856-0.30970.5271.25940.1410.2220.69750.0911.627655.418-18.9989-12.9358
119.1091.4787-0.25455.33972.21117.2075-0.4237-0.9513-0.15960.7080.06390.25810.43090.84490.32290.89150.22490.20031.10890.38511.37368.0429-9.5262-14.127
123.224-3.074-0.4614.21123.38156.9051-0.10250.2123-0.48170.03910.0284-0.13670.34650.23390.10050.9089-0.11680.14140.7243-0.02831.19456.8386-8.0685-40.807
137.48073.2178-0.84286.4260.02596.7057-0.1637-0.2889-0.41240.40840.1216-0.6505-0.36480.37790.08250.81020.0265-0.03150.6584-0.03621.145242.679410.6941-15.749
143.1706-3.64452.60634.2657-4.37098.4058-0.07470.38260.1036-0.2461-0.4282-0.25470.14150.26830.49470.7545-0.02940.09730.6965-0.05781.153350.78412.4875-41.5968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 113 through 124 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 230 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 339 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 115 through 223 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 224 through 338 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 116 through 230 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 231 through 336 )C0
8X-RAY DIFFRACTION8chain 'D' and (resid 116 through 230 )D0
9X-RAY DIFFRACTION9chain 'D' and (resid 231 through 337 )D0
10X-RAY DIFFRACTION10chain 'E' and (resid 115 through 161 )E0
11X-RAY DIFFRACTION11chain 'E' and (resid 162 through 230 )E0
12X-RAY DIFFRACTION12chain 'E' and (resid 231 through 337 )E0
13X-RAY DIFFRACTION13chain 'F' and (resid 116 through 230 )F0
14X-RAY DIFFRACTION14chain 'F' and (resid 231 through 338 )F0

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