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- PDB-6w0j: Closed-gate KcsA incubated in BaCl2/NaCl -

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Basic information

Entry
Database: PDB / ID: 6w0j
TitleClosed-gate KcsA incubated in BaCl2/NaCl
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: 2.5 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_asym_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_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_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_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

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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)57,9634
Polymers57,8263
Non-polymers1371
Water1,58588
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)231,85216
Polymers231,30312
Non-polymers5494
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
Buried area31440 Å2
ΔGint-222 kcal/mol
Surface area86020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.329, 156.329, 76.359
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-306-

HOH

31C-313-

HOH

41C-314-

HOH

51C-323-

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-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 4.03 Å3/Da / Density % sol: 69.51 %
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: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→68.612 Å / Num. obs: 32029 / % possible obs: 99.9 % / Redundancy: 9.6 % / CC1/2: 0.99 / Net I/σ(I): 7.1
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 3625 / CC1/2: 0.55

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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: 2.5→68.612 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.89
RfactorNum. reflection% reflection
Rfree0.2184 1606 5.02 %
Rwork0.19 --
obs0.1914 32018 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.46 Å2 / Biso mean: 63.9603 Å2 / Biso min: 17.79 Å2
Refinement stepCycle: final / Resolution: 2.5→68.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 1 88 4105
Biso mean--34.79 52.87 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084120
X-RAY DIFFRACTIONf_angle_d0.9575635
X-RAY DIFFRACTIONf_dihedral_angle_d3.9332409
X-RAY DIFFRACTIONf_chiral_restr0.052646
X-RAY DIFFRACTIONf_plane_restr0.006714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.5001-2.58080.28661380.26872760
2.5808-2.67310.27231350.2582751
2.6731-2.78010.30111620.2492737
2.7801-2.90660.27811290.22272758
2.9066-3.05990.2211480.2052761
3.0599-3.25160.22451360.20032767
3.2516-3.50260.21971550.18442722
3.5026-3.85510.21491370.17482769
3.8551-4.41280.20761580.16152754
4.4128-5.55930.18511410.16322807
5.5593-68.6120.2011670.19272826
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)
13.25061.3789-2.23911.5888-1.02443.2187-0.3081-0.0128-0.5204-0.14980.10.02290.8926-0.36730.28360.6632-0.20210.01280.39050.04940.5039134.762118.507-6.365
22.34191.0232-1.33391.2808-1.41093.15910.1308-0.4601-0.18360.3096-0.03890.24130.1898-0.2839-0.09250.4953-0.15350.04830.51160.06340.3773130.537130.3385.837
31.3764-0.3820.4282.0414-1.15252.8422-0.05290.18520.0223-0.24940.00250.03710.1556-0.14280.060.2607-0.0447-0.00710.2427-0.05180.2253150.641146.194-43.689
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 22:124 )C22 - 124

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