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- PDB-5ebm: KcsA T75G mutant in the nonconductive state -

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Basic information

Entry
Database: PDB / ID: 5ebm
TitleKcsA T75G mutant in the nonconductive 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: 2.5 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: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)60,9438
Polymers60,0573
Non-polymers8875
Water1,31573
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)243,77332
Polymers240,22612
Non-polymers3,54620
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_595-x,-y+4,z1
crystal symmetry operation3_775-y+2,x+2,z1
crystal symmetry operation4_375y-2,-x+2,z1
Unit cell
Length a, b, c (Å)155.720, 155.720, 75.556
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-1003-

K

21C-1004-

K

31C-1005-

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: 23296.154 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, 78 molecules

#4: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#5: Chemical ChemComp-F09 / NONAN-1-OL


Mass: 144.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H20O
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 69.11 %
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 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→55.054 Å / Num. all: 31464 / Num. obs: 31464 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 50.26 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.035 / Rrim(I) all: 0.092 / Rsym value: 0.085 / Net I/av σ(I): 8.287 / Net I/σ(I): 15.6 / Num. measured all: 219611
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
2.5-2.646.21.1240.72831745630.4931.1241.5100
2.64-2.87.20.7191.13098543300.290.7192.5100
2.8-2.996.80.4011.92770740730.1670.4014.5100
2.99-3.236.70.2093.72557337960.0870.2098.5100
3.23-3.547.20.1226.32496334740.0490.12215100
3.54-3.957.30.089.32312131580.0320.0822.5100
3.95-4.567.40.051142055327900.020.05133.5100
4.56-5.597.30.04415.91747923870.0170.04436.9100
5.59-7.917.30.042161350818480.0170.04235.1100
7.91-55.0547.10.02722.1740510450.0110.02751.499.4

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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: 2.5→42.783 Å / FOM work R set: 0.7901 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 2991 10.14 %
Rwork0.2158 26505 -
obs0.2194 29496 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.61 Å2 / Biso mean: 31.26 Å2 / Biso min: 3.83 Å2
Refinement stepCycle: final / Resolution: 2.5→42.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3981 0 44 73 4098
Biso mean--82.02 25.69 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034082
X-RAY DIFFRACTIONf_angle_d0.5825574
X-RAY DIFFRACTIONf_chiral_restr0.04644
X-RAY DIFFRACTIONf_plane_restr0.003706
X-RAY DIFFRACTIONf_dihedral_angle_d9.7391410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.54110.39831180.33651022114076
2.5411-2.58490.39081370.32321091122883
2.5849-2.63190.32241200.29661122124284
2.6319-2.68250.37271260.2881167129387
2.6825-2.73730.37941390.28391170130988
2.7373-2.79680.31921270.27561197132490
2.7968-2.86180.31231480.25891218136692
2.8618-2.93340.27941480.2621239138792
2.9334-3.01270.29671310.26391266139793
3.0127-3.10130.34521430.24931263140696
3.1013-3.20140.2911280.24241324145297
3.2014-3.31580.28531590.24991301146097
3.3158-3.44850.27361460.22721317146398
3.4485-3.60530.22121460.22461338148499
3.6053-3.79530.23251640.20991297146199
3.7953-4.03290.25661340.2011377151199
4.0329-4.3440.23261660.193313161482100
4.344-4.78070.22451490.171813571506100
4.7807-5.47120.19641380.175213681506100
5.4712-6.88850.22021810.186413571538100
6.8885-42.78960.19611430.20041398154199

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