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- PDB-3ldd: High resolution open MthK pore structure crystallized in 100 mM K... -

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Basic information

Entry
Database: PDB / ID: 3ldd
TitleHigh resolution open MthK pore structure crystallized in 100 mM K+ and further soaked in 99 mM Na+/1 mM K+.
ComponentsCalcium-gated potassium channel mthK
KeywordsTRANSPORT PROTEIN / transmembrane / ion channel / open conformation / potassium / ion transport / Alternative initiation / Cell membrane / Ionic channel / Membrane / Metal-binding / Potassium transport / Transport
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 / 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. / Helix Hairpins - #70 / Potassium channel 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. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / NAD(P)-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Calcium-gated potassium channel MthK
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYe, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Novel insights into K(+) selectivity from high-resolution structures of an open K(+) channel pore.
Authors: Ye, S. / Li, Y. / Jiang, Y.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2496
Polymers9,0541
Non-polymers1955
Water1,00956
1
A: Calcium-gated potassium channel mthK
hetero molecules

A: Calcium-gated potassium channel mthK
hetero molecules

A: Calcium-gated potassium channel mthK
hetero molecules

A: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,99624
Polymers36,2154
Non-polymers78220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area6140 Å2
ΔGint-73 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.323, 63.323, 44.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1-

K

21A-2-

K

31A-3-

K

41A-4-

K

51A-5-

K

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Components

#1: Protein Calcium-gated potassium channel mthK


Mass: 9053.629 Da / Num. of mol.: 1 / Fragment: MthK K+ channel, residues 28-99 / Mutation: S68R, V77C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: mthK, MTH_1520 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: O27564
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 3.0-3.5 M 1,6-Hexandiol, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 16086 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 31.5 Å2 / Rsym value: 0.047 / Net I/σ(I): 57.2
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.3 / Num. unique all: 616 / Rsym value: 0.509 / % possible all: 76.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MthK pore crystallized in 100 mM K+

Resolution: 1.45→25.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.463 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21571 1636 10.2 %RANDOM
Rwork0.19074 ---
obs0.19315 14429 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.548 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2--0.61 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.45→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms641 0 5 56 702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022659
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.96904
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.909581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.68820.90922
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8331596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.294153
X-RAY DIFFRACTIONr_chiral_restr0.0670.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02479
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.2333
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.2487
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.030.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5980.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.030.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.5404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1952659
X-RAY DIFFRACTIONr_scbond_it1.8193260
X-RAY DIFFRACTIONr_scangle_it2.6794.5245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 103 -
Rwork0.253 871 -
obs--80.96 %
Refinement TLS params.Method: refined / Origin x: 4.4324 Å / Origin y: 18.8894 Å / Origin z: -4.2379 Å
111213212223313233
T0.0187 Å20.0066 Å2-0.0258 Å2--0.0061 Å2-0.0075 Å2---0.0036 Å2
L0.6608 °2-0.5605 °20.138 °2-0.5829 °2-0.4334 °2--0.9602 °2
S-0.017 Å °-0.0348 Å °0.0049 Å °-0.0198 Å °0.0476 Å °0.0338 Å °0.0875 Å °0.082 Å °-0.0306 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 42
2X-RAY DIFFRACTION1A43 - 68
3X-RAY DIFFRACTION1A69 - 83
4X-RAY DIFFRACTION1A84 - 99
5X-RAY DIFFRACTION1K1
6X-RAY DIFFRACTION1K2
7X-RAY DIFFRACTION1K3
8X-RAY DIFFRACTION1K4
9X-RAY DIFFRACTION1K5

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