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- PDB-1lnq: CRYSTAL STRUCTURE OF MTHK AT 3.3 A -

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Basic information

Entry
Database: PDB / ID: 1lnq
TitleCRYSTAL STRUCTURE OF MTHK AT 3.3 A
ComponentsPOTASSIUM CHANNEL RELATED PROTEIN
KeywordsMETAL TRANSPORT / rossmann fold / helix bundle / membrane protein
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 / 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. / Helix Hairpins - #70 ...Voltage-gated potassium channel / Regulator of K+ conductance, C-terminal domain / 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. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Up-down Bundle / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 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 / MIR / Resolution: 3.3 Å
AuthorsJiang, Y. / Lee, A. / Chen, J. / Cadene, M. / Chait, B.T. / Mackinnon, R.
Citation
Journal: Nature / Year: 2002
Title: CRYSTAL STRUCTURE AND MECHANISM OF A CALCIUM-GATED POTASSIUM CHANNEL
Authors: JIANG, Y. / LEE, A. / CHEN, J. / CADENE, M. / CHAIT, B.T. / MACKINNON, R.
#1: Journal: Nature / Year: 2002
Title: THE OPEN PORE CONFORMATION OF POTASSIUM CHANNELS
Authors: JIANG, Y. / LEE, A. / CHEN, J. / CADENE, M. / CHAIT, B.T. / MACKINNON, R.
History
DepositionMay 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: POTASSIUM CHANNEL RELATED PROTEIN
B: POTASSIUM CHANNEL RELATED PROTEIN
C: POTASSIUM CHANNEL RELATED PROTEIN
D: POTASSIUM CHANNEL RELATED PROTEIN
E: POTASSIUM CHANNEL RELATED PROTEIN
F: POTASSIUM CHANNEL RELATED PROTEIN
G: POTASSIUM CHANNEL RELATED PROTEIN
H: POTASSIUM CHANNEL RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,17016
Polymers298,8498
Non-polymers3218
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40390 Å2
ΔGint-337 kcal/mol
Surface area105650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)137.000, 137.000, 373.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
POTASSIUM CHANNEL RELATED PROTEIN / mthk channels


Mass: 37356.160 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mth1520 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): xl1blue / References: UniProt: O27564
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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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: 3.38 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEGMME350, CaCl2, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMLDAO1drop
220 mMTris1droppH8.0
3100 mM1dropKCl
415.0 mg/mlprotein1drop
523-26 %PEG350 MME1reservoir
6100 mMMES1reservoirpH6.5
7200 mM1reservoirCaCl2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONALS 5.0.221
SYNCHROTRONCHESS F130.95
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
211
30.951
ReflectionResolution: 3.3→50 Å / Num. all: 59900 / Num. obs: 56550 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.12
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1 / Num. unique all: 4224 / Rsym value: 0.55 / % possible all: 71
Reflection
*PLUS
Lowest resolution: 50 Å

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Processing

Software
NameVersionClassification
SHARPphasing
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 3.3→46.45 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.318 2869 5.1 %RANDOM
Rwork0.301 ---
obs0.301 56550 95.3 %-
all-59900 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0014 Å2 / ksol: 0.245281 e/Å3
Displacement parametersBiso mean: 84.7 Å2
Baniso -1Baniso -2Baniso -3
1-16.91 Å218.33 Å20 Å2
2--16.91 Å20 Å2
3----33.82 Å2
Refine analyzeLuzzati coordinate error free: 0.54 Å / Luzzati sigma a free: 0.9 Å
Refinement stepCycle: LAST / Resolution: 3.3→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16888 0 8 0 16896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 405 5.3 %
Rwork0.395 7222 -
obs--77.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
Refinement
*PLUS
Rfactor obs: 0.299 / Rfactor Rfree: 0.315 / Rfactor Rwork: 0.299
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.413 / Rfactor Rwork: 0.395 / Rfactor obs: 0.395

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