PDB-4qe9: Open MthK pore structure soaked in 10 mM Ba2+/100 mM K+

Basic information

• Entry: Database: PDB / ID: 4qe9
• Title: Open MthK pore structure soaked in 10 mM Ba2+/100 mM K+
• Components: Calcium-gated potassium channel MthK
• Keywords: TRANSPORT PROTEIN / Transmembrane / Ion channel / Open conformation

Function / homology

Function:

monoatomic cation transmembrane transporter activity / potassium ion transport / metal ion binding / identical protein binding / plasma membrane

Domain/homology:

: / 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

Component:

: / Calcium-gated potassium channel MthK

• Biological species: Methanothermobacter thermautotrophicus (archaea)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
• Authors: Guo, R. / Zeng, W. / Cui, H. / Chen, L. / Ye, S.
• Citation: Journal: J.Gen.Physiol. / Year: 2014; Title: Ionic interactions of Ba2+ blockades in the MthK K+ channel; Authors: Guo, R. / Zeng, W. / Cui, H. / Chen, L. / Ye, S.

History

Deposition	May 15, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Jul 9, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 10, 2014	Group: Database references
Revision 1.2	Nov 8, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Calcium-gated potassium channel MthK

hetero molecules

Summary:

• 9.38 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	9,383	7
Polymers	9,149	1
Non-polymers	235	6
Water	775	43

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

Summary:

• defined by author&software
• 37.5 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	37,533	28
Polymers	36,595	4
Non-polymers	938	24
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_655	-x+1,-y,z	1
crystal symmetry operation	3_545	-y+1/2,x-1/2,z	1
crystal symmetry operation	4_555	y+1/2,-x+1/2,z	1

Calculated values:

Buried area	6080 Å2
ΔGint	-72 kcal/mol
Surface area	15470 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	61.005, 61.005, 44.950
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P4212

Components on special symmetry positions

ID	Model	Components
1	1	A-201- K
2	1	A-202- K
3	1	A-203- K
4	1	A-204- K
5	1	A-205- K
6	1	A-206- K

Components

#1: Protein

A Calcium-gated potassium channel MthK

Details:

Mass: 9148.686 Da / Num. of mol.: 1 / Fragment: UNP residues 18-100 / Mutation: S51H, V60C
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

A-201 A-202 A-203 A-204 A-205 A-206
ChemComp-K / POTASSIUM ION

Details:

Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.29 ų/Da / Density % sol: 46.19 %
• Crystal grow: Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 ; Details: 3.0-3.5M 1,6-Hexandiol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9786 Å
• Detector: Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2013
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 0.9786 Å / Relative weight: 1
• Reflection: Resolution: 2.15→50 Å / Num. obs: 4888 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 10.5 % / R_merge(I) obs: 0.105 / Net I/σ(I): 26.6

Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LDC

3ldc

Resolution: 2.15→30.5 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.91 / SU B: 10.884 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.25673	478	9.8 %	RANDOM
Rwork	0.1981	-	-	-
obs	0.20392	4389	100 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 51.793 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.69 Å2	0 Å2	0 Å2
2-	-	-0.69 Å2	0 Å2
3-	-	-	1.39 Å2

Refinement step

Cycle: LAST / Resolution: 2.15→30.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	648	0	6	43	697

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	667
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.149	1.95	916
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.596	5	82
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.916	21.739	23
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.11	15	95
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.26	15	2
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	113
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	488
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	361
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	488
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.144	0.2	40
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined	0.001	0.2	1
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.451	0.2	77
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.138	0.2	6
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.001	0.2	3
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.523	1.5	409
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.984	2	667
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.399	3	263
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.188	4.5	249
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.15→2.208 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.409	31	-
Rwork	0.243	322	-
obs	-	-	100 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.503	1.1551	-2.5794	2.7699	-2.8934	19.1667	0.1302	-0.0728	0.2861	0.1057	-0.1648	0.3711	0.4777	0.7595	0.0346	-0.0976	-0.0251	0.0133	-0.0735	-0.016	0.0007	11.9353	-4.2624	20.2995
2	2.7239	-0.9992	0.4684	0.8452	-1.2045	2.3084	-0.0064	0.1123	-0.1588	-0.0365	0.0269	0.0703	0.0662	-0.1076	-0.0205	-0.015	-0.0351	0.0036	-0.0521	-0.0071	-0.0583	19.6274	-3.8643	10.4169
3	3.5503	-4.966	6.4263	11.8647	-14.1309	17.008	0.1016	-0.3966	-0.1351	0.0788	0.2381	0.3776	-0.0641	-0.3781	-0.3397	-0.055	0.0039	0.0279	0.0001	0.0132	-0.0663	19.8018	-1.9727	23.5661

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	19 - 42
2	X-RAY DIFFRACTION	2	A	43 - 69
3	X-RAY DIFFRACTION	3	A	70 - 99