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- PDB-5ebl: KcsA T75G in the Conductive State -

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Basic information

Entry
Database: PDB / ID: 5ebl
TitleKcsA T75G in the Conductive State
Components
  • (Antibody Fab Fragment Light ...) x 2
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / alpha-helical / Fab / 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
DIACYL GLYCEROL / NONAN-1-OL / : / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesMus musculus (house mouse)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Model detailsmutant1
AuthorsMatulef, K. / Valiyaveetil, F.I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2016
Title: Individual Ion Binding Sites in the K(+) Channel Play Distinct Roles in C-type Inactivation and in Recovery from Inactivation.
Authors: Matulef, K. / Annen, A.W. / Nix, J.C. / Valiyaveetil, F.I.
History
DepositionOct 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_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_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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,17611
Polymers60,1723
Non-polymers1,0048
Water3,117173
1
A: Antibody Fab Fragment Light Chain
B: Antibody Fab Fragment Light Chain
C: pH-gated potassium channel KcsA
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)244,70244
Polymers240,68712
Non-polymers4,01532
Water21612
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
Unit cell
Length a, b, c (Å)155.410, 155.410, 76.273
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-1002-

K

21C-1003-

K

31C-1004-

K

41C-1005-

K

51C-1006-

K

61C-1007-

K

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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: 13324.719 Da / Num. of mol.: 1 / Fragment: UNP residues 1-125 / Mutation: T75G
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 Antibody Fab Fragment Light Chain


Mass: 23411.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody Antibody Fab Fragment Light Chain


Mass: 23435.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hybridoma / Production host: Mus musculus (house mouse)

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Non-polymers , 4 types, 181 molecules

#4: Chemical ChemComp-F09 / NONAN-1-OL


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#5: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 400

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→54.947 Å / Num. all: 40541 / Num. obs: 40541 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Rsym value: 0.109 / Net I/av σ(I): 6.457 / Net I/σ(I): 13.1 / Num. measured all: 290580
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.427.11.2910.64152858790.5231.2911.5100
2.42-2.5770.8850.93918655670.3590.8852.2100
2.57-2.756.70.5451.43494852440.2290.5453.4100
2.75-2.976.90.3292.33376448900.1350.3295.9100
2.97-3.257.50.184.33354544870.0710.1811100
3.25-3.647.50.1037.43083040980.0410.10318.2100
3.64-4.27.50.06611.12675435890.0260.06626.9100
4.2-5.147.40.04714.42275530650.0180.04735.9100
5.14-7.277.40.048141768923870.0190.04831.8100
7.27-54.9477.20.03416.3958113350.0140.03443.199.7

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 2.3→38.852 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 3782 10.05 %
Rwork0.2048 --
obs0.2085 37615 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.36 Å2 / Biso mean: 46.6517 Å2 / Biso min: 16.21 Å2
Refinement stepCycle: final / Resolution: 2.3→38.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3996 0 47 173 4216
Biso mean--65.84 46.25 -
Num. residues----534

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