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- PDB-6w0g: Closed-gate KcsA soaked in 1mM KCl/5mM BaCl2 -

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Basic information

Entry
Database: PDB / ID: 6w0g
TitleClosed-gate KcsA soaked in 1mM KCl/5mM BaCl2
Components
  • Fab Heavy ChainFragment antigen-binding
  • Fab Light ChainFragment antigen-binding
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / Ion channel
Function / homology
Function and homology information


monoatomic ion transmembrane transport / identical protein binding / plasma membrane
Similarity search - Function
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 speciesRattus norvegicus (Norway rat)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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

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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)57,8654
Polymers57,8263
Non-polymers391
Water77543
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)231,45916
Polymers231,30312
Non-polymers1564
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)155.138, 155.138, 75.380
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-308-

HOH

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Components

#1: Antibody Fab Heavy Chain / Fragment antigen-binding


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 / Fragment antigen-binding


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.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


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

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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: 3.92 Å3/Da / Density % sol: 68.64 %
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: 2.6→54.85 Å / Num. obs: 27029 / % possible obs: 97.6 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 3331 / CC1/2: 0.13

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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: 2.6→54.85 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.69
RfactorNum. reflection% reflection
Rfree0.2448 1364 5.06 %
Rwork0.1962 --
obs0.1986 26980 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.57 Å2 / Biso mean: 70.4394 Å2 / Biso min: 28.03 Å2
Refinement stepCycle: final / Resolution: 2.6→54.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 1 45 4062
Biso mean--65.06 60.4 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084120
X-RAY DIFFRACTIONf_angle_d0.9835635
X-RAY DIFFRACTIONf_dihedral_angle_d3.7362409
X-RAY DIFFRACTIONf_chiral_restr0.053646
X-RAY DIFFRACTIONf_plane_restr0.006714
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6001-2.6930.40411380.3607257998
2.693-2.80090.37441540.3323250497
2.8009-2.92830.35961530.2882247496
2.9283-3.08270.32261500.2669256899
3.0827-3.27580.29241330.2322258598
3.2758-3.52870.29721360.2062250696
3.5287-3.88370.22141190.1846261599
3.8837-4.44550.21031370.1578262398
4.4455-5.60.20811170.1474255896
5.6-54.850.18261270.179260496
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)
11.9090.5725-1.50051.3046-0.67662.9268-0.28810.1035-0.1309-0.12410.09-0.17810.7764-0.3591-0.00670.6386-0.2069-0.03170.3187-0.00380.3612133.9603117.2085-6.4204
21.44650.3836-0.82911.0737-0.86522.24760.0139-0.22240.08470.22620.0287-0.01940.2379-0.37410.00010.5481-0.1447-0.07720.4832-0.01670.3734129.5422129.1095.8366
30.9690.218-1.18621.20110.0071.373-0.05220.19810.2204-0.25410.21080.2180.2136-0.56280.00080.2848-0.0744-0.09440.30280.09140.4839149.573144.89-43.6848
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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