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- PDB-6w0d: Open-gate KcsA soaked in 5 mM BaCl2 -

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Basic information

Entry
Database: PDB / ID: 6w0d
TitleOpen-gate KcsA soaked in 5 mM 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: 3.639 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 / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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_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_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 16, 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)56,7505
Polymers56,5733
Non-polymers1762
Water905
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)226,99920
Polymers226,29312
Non-polymers7068
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area30040 Å2
ΔGint-187 kcal/mol
Surface area84630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.912, 156.912, 73.671
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-

BA

21C-202-

K

31C-301-

HOH

41C-302-

HOH

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Components

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Protein , 1 types, 1 molecules C

#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 9726.300 Da / Num. of mol.: 1
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

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Antibody , 2 types, 2 molecules AB

#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)

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Non-polymers , 3 types, 7 molecules

#4: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.01 Å3/Da / Density % sol: 69.31 %
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-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.6→55.477 Å / Num. obs: 10018 / % possible obs: 97.9 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.25 / Net I/σ(I): 7.2
Reflection shellResolution: 3.6→3.7 Å / Num. unique obs: 2204 / CC1/2: 0.36

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 3.639→55.477 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 537 5.38 %
Rwork0.1902 9452 -
obs0.1933 9989 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 302 Å2 / Biso mean: 130.6947 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.639→55.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3938 0 2 5 3945
Biso mean--25.1 30 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044063
X-RAY DIFFRACTIONf_angle_d0.7765553
X-RAY DIFFRACTIONf_dihedral_angle_d3.8792380
X-RAY DIFFRACTIONf_chiral_restr0.044639
X-RAY DIFFRACTIONf_plane_restr0.005703
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.639-4.00510.31541320.2866216191
4.0051-4.58440.29871250.19922418100
4.5844-5.77490.24791440.18122409100
5.7749-55.470.20851360.16312464100
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)
12.40570.6923-2.43922.5594-0.57834.8761-0.47420.0896-0.36970.10080.1035-0.29211.7305-0.87750.39061.6436-0.4582-0.06060.94730.02711.1129-21.24-38.444-8.86
21.79771.0396-2.84392.295-1.24985.4802-0.075-0.29310.02630.5386-0.0259-0.05830.7554-0.484-0.11581.0906-0.3457-0.07161.17210.09150.9329-25.823-26.4413.343
35.03-1.15620.49185.257-1.44278.35920.18160.9225-0.0745-0.9423-0.00030.4066-0.2681-0.5257-0.17230.7604-0.0589-0.00010.7998-0.1080.9887-7.09-10.266-42.691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:219 )A1 - 219
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:212 )B1 - 212
3X-RAY DIFFRACTION3( CHAIN C AND RESID 28:120 )C28 - 120

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