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- PDB-6w0i: Closed-gate KcsA soaked in 10mM KCl/5mM BaCl2 -

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Basic information

Entry
Database: PDB / ID: 6w0i
TitleClosed-gate KcsA soaked in 10mM KCl/5mM BaCl2
Components
  • Fab Heavy Chain
  • Fab Light Chain
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / Ion channel
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.328 Å
AuthorsRohaim, A. / Gong, L. / Li, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Open and Closed Structures of a Barium-Blocked Potassium Channel.
Authors: Rohaim, A. / Gong, L. / Li, J. / Rui, H. / Blachowicz, L. / Roux, B.
History
DepositionFeb 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 19, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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.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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab Heavy Chain
B: Fab Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0609
Polymers57,8263
Non-polymers2356
Water1,15364
1
A: Fab Heavy Chain
B: Fab Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab Heavy Chain
B: Fab Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab Heavy Chain
B: Fab Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

A: Fab Heavy Chain
B: Fab Light Chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,24136
Polymers231,30312
Non-polymers93824
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-y+2,x,z1
crystal symmetry operation4_575y,-x+2,z1
Unit cell
Length a, b, c (Å)154.238, 154.238, 75.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-201-

K

21C-202-

K

31C-203-

K

41C-204-

K

51C-205-

K

61C-206-

K

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Components

#1: Antibody Fab Heavy Chain


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#2: Antibody Fab Light Chain


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Homo sapiens (human)
#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 10978.736 Da / Num. of mol.: 1 / Mutation: L90C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.89 Å3/Da / Density % sol: 68.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20 % PEG 400, 50 mM Magnesium Acetate, 50 mM Sodium Acetate, pH 5.5

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→67.971 Å / Num. obs: 37609 / % possible obs: 98.6 % / Redundancy: 10.6 % / CC1/2: 0.92 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.4 Å / Num. unique obs: 3385 / CC1/2: 0.29

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k4c

1k4c


Resolution: 2.328→67.971 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.83
RfactorNum. reflection% reflection
Rfree0.2319 1859 4.95 %
Rwork0.2003 --
obs0.2019 37556 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.15 Å2 / Biso mean: 70.5412 Å2 / Biso min: 27.02 Å2
Refinement stepCycle: final / Resolution: 2.328→67.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4020 0 6 64 4090
Biso mean--54.81 56.98 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084125
X-RAY DIFFRACTIONf_angle_d0.9535641
X-RAY DIFFRACTIONf_dihedral_angle_d3.5762410
X-RAY DIFFRACTIONf_chiral_restr0.052646
X-RAY DIFFRACTIONf_plane_restr0.005714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3282-2.39120.39731460.3389240788
2.3912-2.46150.34951210.3218279599
2.4615-2.5410.34341450.2769276399
2.541-2.63180.30191350.2432748100
2.6318-2.73720.26441490.23582770100
2.7372-2.86180.30561450.232273898
2.8618-3.01260.24831700.20772741100
3.0126-3.20140.25671080.1922818100
3.2014-3.44850.26311320.1894274999
3.4485-3.79560.19781450.175279999
3.7956-4.34470.21291580.17082794100
4.3447-5.47350.18471430.1778277798
5.4735-67.9710.21621620.2013279898
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)
12.02410.8836-1.38351.1184-0.45482.4724-0.1737-0.0596-0.3203-0.09130.0234-0.00860.8527-0.22730.00960.7112-0.18790.03850.38870.04590.5132133.1634116.5781-6.493
21.32010.5476-0.57331.262-0.71392.02470.0677-0.3332-0.12090.2565-0.03910.10280.275-0.2432-0.00080.5796-0.1530.02990.59620.0640.4426128.7433128.37265.9021
30.7280.2750.06490.23920.47061.3216-0.08780.1143-0.04350.06070.07470.0265-0.0531-0.1154-00.3141-0.0305-0.00040.3098-0.02480.362148.6192144.2459-43.8662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:219)A1 - 219
2X-RAY DIFFRACTION2(chain B and resseq 1:212)B1 - 212
3X-RAY DIFFRACTION3(chain C and resseq 22:124)C22 - 124

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