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- PDB-3kxd: Crystal structure of the mthk rck in complex with cadmium -

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Basic information

Entry
Database: PDB / ID: 3kxd
TitleCrystal structure of the mthk rck in complex with cadmium
ComponentsCalcium-gated potassium channel mthK
KeywordsTRANSPORT PROTEIN / RCK / MTHK / CADMIUM / POTASSIUM CHANNEL / ALTERNATIVE INITIATION / ION TRANSPORT / IONIC CHANNEL / MEMBRANE / METAL-BINDING / POTASSIUM / POTASSIUM TRANSPORT / TRANSMEMBRANE / TRANSPORT / Cell membrane
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. / Potassium channel domain ...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. / 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 str. Delta H (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsDvir, H. / Choe, S.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: Structure of the MthK RCK in complex with cadmium.
Authors: Dvir, H. / Valera, E. / Choe, S.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / 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 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Calcium-gated potassium channel mthK
B: Calcium-gated potassium channel mthK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1326
Polymers49,6832
Non-polymers4504
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-76 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.022, 38.293, 96.634
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGPHEPHEAA116 - 2321 - 117
21ARGARGPHEPHEBB116 - 2321 - 117
12VALVALALAALAAA233 - 257118 - 142
22VALVALALAALABB233 - 257118 - 142
13SERSERILEILEAA260 - 334145 - 219
23SERSERILEILEBB260 - 334145 - 219

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Calcium-gated potassium channel mthK / MTHK


Mass: 24841.270 Da / Num. of mol.: 2 / Fragment: RCK DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea)
Gene: mthK, MTH_1520 / Plasmid: PQE70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: O27564
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 318 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1M NH4-FORMATE, 10% PEG 4000, 0.1M NA ACETATE, PH 4.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 318K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2008 / Details: FLAT MIRROR, RH COATED
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→57.83 Å / Num. obs: 21805 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 10.8

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2AEJ

2aej


Resolution: 2.2→57.83 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.906 / SU B: 13.329 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25364 1108 5.1 %RANDOM
Rwork0.1844 ---
obs0.1878 20697 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.557 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-1.02 Å2
2--0.41 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3378 0 4 112 3494
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9764630
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6195441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50323.725153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50315601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5561534
X-RAY DIFFRACTIONr_chiral_restr0.140.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02670
X-RAY DIFFRACTIONr_nbd_refined0.2350.2747
X-RAY DIFFRACTIONr_nbd_other0.210.22471
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21616
X-RAY DIFFRACTIONr_nbtor_other0.0950.21908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2950.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3190.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9621.52192
X-RAY DIFFRACTIONr_mcbond_other0.3351.5905
X-RAY DIFFRACTIONr_mcangle_it1.69623539
X-RAY DIFFRACTIONr_scbond_it2.8831229
X-RAY DIFFRACTIONr_scangle_it4.7154.51091
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1468MEDIUM POSITIONAL0.270.5
1427LOOSE POSITIONAL0.695
1468MEDIUM THERMAL1.262
1427LOOSE THERMAL1.910
2100MEDIUM POSITIONAL0.110.5
292LOOSE POSITIONAL0.515
2100MEDIUM THERMAL0.712
292LOOSE THERMAL1.3510
3300MEDIUM POSITIONAL0.180.5
3250LOOSE POSITIONAL0.535
3300MEDIUM THERMAL0.82
3250LOOSE THERMAL110
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 91 -
Rwork0.191 1525 -
obs--98.6 %
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)
13.5766-0.3707-1.16583.7598-1.15364.65790.1336-0.07830.06980.06010.12780.2445-0.345-0.1143-0.26140.20490.01870.06780.03660.01990.106920.2052.1827.997
28.32520.17860.32990.3331-0.70649.9367-0.0299-0.62070.05580.2445-0.1666-0.037-0.6999-0.02650.19650.34820.01940.04770.46110.16320.28015.034-7.61426.704
38.58980.4709-3.23184.45163.785913.19020.1684-1.77460.17730.20670.3934-0.2365-0.2452.1252-0.56190.466-0.08840.03820.9006-0.05330.241927.754-4.37936.538
414.4632-1.0169-1.99162.77251.13914.2753-0.19630.2497-1.12590.0003-0.20610.37380.2891-0.30570.40230.271-0.02940.05570.2992-0.03120.3548-7.383-10.73616.609
52.881-0.947-0.52793.5172-1.04534.6360.0988-0.1826-0.14330.20980.05930.29920.4042-0.2217-0.15810.3297-0.04040.05620.23340.03950.128516.765-6.69322.365
611.9728-1.7212-0.03383.9984-0.200910.31690.0591-2.1398-0.63290.28650.06380.21180.5354-0.7162-0.12280.4807-0.1430.05211.01220.25180.39067.788-13.98342.976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 232
2X-RAY DIFFRACTION2A233 - 257
3X-RAY DIFFRACTION3A258 - 339
4X-RAY DIFFRACTION4B116 - 232
5X-RAY DIFFRACTION5B233 - 259
6X-RAY DIFFRACTION6B260 - 334

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