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- PDB-4l74: Ca2+-bound MthK RCK domain at 1.9 Angstrom with single ligand -

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Basic information

Entry
Database: PDB / ID: 4l74
TitleCa2+-bound MthK RCK domain at 1.9 Angstrom with single ligand
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: 1.841 Å
AuthorsSmith, F.J. / Cingolani, G. / 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.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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)53,8554
Polymers53,7752
Non-polymers802
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-65 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.233, 38.424, 96.821
Angle α, β, γ (deg.)90.000, 94.320, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.01 Å3/Da / Density % sol: 38.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 6% 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: X6A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 19, 2011
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.841→15 Å / Num. all: 35686 / Num. obs: 35686 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.068 / Χ2: 1.991 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.841-1.924.20.33635232.141196.1
1.92-1.994.30.39735382.112196.9
1.99-2.084.60.26135891.563198
2.08-2.194.60.19935761.68198.2
2.19-2.333.80.15632772.533189.3
2.33-2.514.60.1236181.896198.6
2.51-2.764.60.08736481.953198.8
2.76-3.164.60.06336532.075199
3.16-3.964.20.04634772.288193.5
3.96-154.40.03637871.903198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AEF

2aef


Resolution: 1.841→14.842 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 29.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1616 5.05 %RANDOM
Rwork0.2106 ---
obs0.2128 34768 89.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.58 Å2 / Biso mean: 40.2489 Å2 / Biso min: 11.5 Å2
Refinement stepCycle: LAST / Resolution: 1.841→14.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3481 0 2 370 3853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073525
X-RAY DIFFRACTIONf_angle_d1.034762
X-RAY DIFFRACTIONf_chiral_restr0.07553
X-RAY DIFFRACTIONf_plane_restr0.003628
X-RAY DIFFRACTIONf_dihedral_angle_d15.9121348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.841-1.86790.3811260.36762334246079
1.8679-1.89710.51831150.46512383249878
1.8971-1.92810.62541190.54231554167352
1.9281-1.96130.65271070.43022396250382
1.9613-1.99690.36421770.28132829300695
1.9969-2.03520.29171340.24992924305897
2.0352-2.07660.26551690.23532890305997
2.0766-2.12160.26641420.22562933307597
2.1216-2.17080.2611490.23442885303497
2.1708-2.2250.30751420.30062617275987
2.225-2.28490.4915730.39241471154450
2.2849-2.35190.33751540.25232863301795
2.3519-2.42750.24441510.21532947309898
2.4275-2.51380.28141660.21752931309798
2.5138-2.6140.23151490.22082933308298
2.614-2.73220.2561600.21042962312298
2.7322-2.87530.27751420.20552926306898
2.8753-3.0540.26511440.20142974311899
3.054-3.28740.24681730.18662938311199
3.2874-3.61390.18651440.16532892303697
3.6139-4.1270.21951270.16882468259582
4.127-5.1630.1671610.14752911307298
5.163-14.84250.19421660.17222882304897
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)
12.28380.537-1.45621.2296-1.16843.23620.14170.03350.13470.033-0.07060.0846-0.20510.0003-0.05260.14280.0019-0.01810.1516-0.0370.114818.91183.98648.4832
25.39571.5518-0.24982.10970.55413.69710.1179-0.56210.42540.07850.0621-0.1465-0.29340.6128-0.15040.3429-0.02430.03720.4132-0.0590.201223.3807-0.260735.4088
33.921.07990.07060.86570.11231.6126-0.06250.0754-0.03580.0395-0.0860.25390.1446-0.4210.14060.2039-0.05170.02570.3566-0.13410.2576-5.7521-7.731716.8684
43.92230.714-1.51542.0737-2.19484.7147-0.1694-0.7785-0.43080.04830.15960.24660.2983-0.27620.02010.3278-0.0392-0.00660.40470.04270.307810.2675-9.589540.6226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 116 through 240 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 241 through 339 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 116 through 240 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 241 through 340 )B0

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