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- PDB-2qto: An anisotropic model for potassium channel KcsA -

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Basic information

Entry
Database: PDB / ID: 2qto
TitleAn anisotropic model for potassium channel KcsA
ComponentsVoltage-gated potassium channel
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN / Potassium channel / membrane proteins / normal-mode refinement / anisotropic thermal factors
Function / homology
Function and homology information


action potential / voltage-gated potassium channel activity / voltage-gated potassium channel complex / identical protein binding
Similarity search - Function
Voltage-gated potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.201 Å
AuthorsChen, X. / Poon, B.K. / Dousis, A. / Wang, Q. / Ma, J.
CitationJournal: Structure / Year: 2007
Title: Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution
Authors: Chen, X. / Poon, B.K. / Dousis, A. / Wang, Q. / Ma, J.
History
DepositionAug 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1297
Polymers41,0124
Non-polymers1173
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.780, 68.930, 112.040
Angle α, β, γ (deg.)90.00, 124.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 1 / Auth seq-ID: 23 - 119 / Label seq-ID: 1 - 97

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Voltage-gated potassium channel / Potassium channel KcsA


Mass: 10252.959 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P0A334
#2: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.99 Å3/Da / Density % sol: 75.34 %
Crystal growpH: 7.5 / Details: 200 MM CACL2, 100 MM HEPES PH 7.5, 48% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 3.201→30 Å / Num. obs: 12603 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 6.1 %

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MIR
Starting model: 1BL8

1bl8


Resolution: 3.201→9.99 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.993 / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27181 1265 10.4 %RANDOM
Rwork0.27162 ---
obs0.27164 10912 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 121.433 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å2-1.64 Å2
2--0.68 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 3.201→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 3 1 2853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222925
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.9344040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg47.92121.56683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.415376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6271511
X-RAY DIFFRACTIONr_chiral_restr0.0570.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022143
X-RAY DIFFRACTIONr_nbd_refined0.2850.21537
X-RAY DIFFRACTIONr_nbtor_refined0.310.22103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2103
X-RAY DIFFRACTIONr_metal_ion_refined0.1080.211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4690.224
Refine LS restraints NCS

Ens-ID: 1 / Number: 710 / Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Dom-IDAuth asym-IDRms dev position (Å)
1A0.09
2B0.15
3C0.09
4D0.1
LS refinement shellResolution: 3.201→3.275 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 51 -
Rwork0.397 520 -
obs--100 %

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