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- PDB-5ec1: KcsA with V76ester mutation -

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Basic information

Entry
Database: PDB / ID: 5ec1
TitleKcsA with V76ester mutation
Components
  • (Antibody Fab Fragment Light ...) x 2
  • pH-gated potassium channel KcsA
KeywordsMEMBRANE PROTEIN / alpha helical / channel / Fab
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: 2.75 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 20, 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.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_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_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.0Aug 13, 2025Group: Data collection / Polymer sequence / Structure summary
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _entity_poly.pdbx_seq_one_letter_code_can

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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)60,76311
Polymers59,7593
Non-polymers1,0048
Water28816
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)243,05344
Polymers239,03712
Non-polymers4,01532
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_355-x-2,-y,z1
crystal symmetry operation3_465-y-1,x+1,z1
crystal symmetry operation4_445y-1,-x-1,z1
Unit cell
Length a, b, c (Å)155.600, 155.600, 75.640
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-2003-

K

21C-2004-

K

31C-2005-

K

41C-2006-

K

51C-2007-

K

61C-2008-

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: 13297.735 Da / Num. of mol.: 1 / Fragment: UNP residues 1-125 / Mutation: V76ester
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: 23050.340 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, 24 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.: 16 / 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: 4 Å3/Da / Density % sol: 69.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG400

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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: Jun 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→55.013 Å / Num. all: 23691 / Num. obs: 23691 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 54.47 Å2 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.055 / Rrim(I) all: 0.212 / Rsym value: 0.204 / Net I/av σ(I): 3.687 / Net I/σ(I): 13.4 / Num. measured all: 344861
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
2.75-2.9142.3560.3124794934360.6532.35647949100
2.9-3.07141.4230.5114555232640.3951.42345552100
3.07-3.2914.40.77714376830480.2120.7773.7100
3.29-3.5514.60.441.84167028470.1190.446.9100
3.55-3.8915.10.26233982926340.070.26211.7100
3.89-4.3515.10.1525.13574623700.040.15219.2100
4.35-5.02150.1017.33172821190.0270.10127.3100
5.02-6.15150.1037.22685017910.0280.10326.7100
6.15-8.714.70.079.92055813940.0190.0735.3100
8.7-55.01314.20.0455.7112117880.0110.0478899.6

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.9_1690refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1K4C

1k4c


Resolution: 2.75→42.776 Å / FOM work R set: 0.7706 / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 2193 10.09 %
Rwork0.2439 19550 -
obs0.2463 21743 91.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.97 Å2 / Biso mean: 36.25 Å2 / Biso min: 0.05 Å2
Refinement stepCycle: final / Resolution: 2.75→42.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 47 16 4023
Biso mean--62.81 33.49 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024063
X-RAY DIFFRACTIONf_angle_d0.5045554
X-RAY DIFFRACTIONf_chiral_restr0.035644
X-RAY DIFFRACTIONf_plane_restr0.003702
X-RAY DIFFRACTIONf_dihedral_angle_d9.2941389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.75-2.80980.36271170.36541018113577
2.8098-2.87520.33931220.35021013113578
2.8752-2.94710.3961130.33391086119982
2.9471-3.02670.34281180.33031102122083
3.0267-3.11580.3431300.3071178130888
3.1158-3.21630.32961260.28141180130690
3.2163-3.33120.31591410.2851225136692
3.3312-3.46450.28461400.27531238137893
3.4645-3.62210.29481360.26261277141395
3.6221-3.8130.2791600.25231244140496
3.813-4.05170.24951220.22681310143297
4.0517-4.36430.24541710.21541288145999
4.3643-4.80290.23921430.194613421485100
4.8029-5.49670.24071350.20851342147799
5.4967-6.92050.23971750.22711321149699
6.9205-42.78130.22241440.22281386153099

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