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- PDB-5ec2: KcsA with V76ester+G77dA mutations -

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Basic information

Entry
Database: PDB / ID: 5ec2
TitleKcsA with V76ester+G77dA mutations
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: 2.3 Å
Model detailsmutant4
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)61,16311
Polymers60,1593
Non-polymers1,0048
Water2,126118
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)244,65044
Polymers240,63512
Non-polymers4,01532
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_535-x,-y-2,z1
crystal symmetry operation3_445-y-1,x-1,z1
crystal symmetry operation4_645y+1,-x-1,z1
Unit cell
Length a, b, c (Å)154.870, 154.870, 75.703
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: 13311.761 Da / Num. of mol.: 1 / Fragment: UNP residues 1-125 / Mutation: V76ester,G77dA
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, 126 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.: 118 / 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: 3.94 Å3/Da / Density % sol: 68.8 %
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: Oct 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→54.755 Å / Num. all: 39959 / Num. obs: 39959 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 43.98 Å2 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.039 / Rrim(I) all: 0.105 / Rsym value: 0.098 / Net I/av σ(I): 6.818 / Net I/σ(I): 12.4 / Num. measured all: 291481
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
2.3-2.426.81.4790.53950858170.6121.4791.2100
2.42-2.577.10.9470.83929455040.3810.9471.9100
2.57-2.757.60.581.43898251290.2260.583.2100
2.75-2.977.70.3332.43699548320.1290.3335.5100
2.97-3.257.60.1754.53350044280.0680.17510.4100
3.25-3.647.40.1027.62966040200.040.10216.9100
3.64-4.27.10.06510.92542935630.0260.06525.4100
4.2-5.147.20.04813.72148029950.0190.04833.8100
5.14-7.277.30.04415.11729223610.0180.04431.9100
7.27-54.7557.10.03318.3934113100.0130.03341.698.7

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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→36.503 Å / FOM work R set: 0.7849 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2591 3628 10.1 %
Rwork0.23 32308 -
obs0.233 35936 89.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.91 Å2 / Biso mean: 51.35 Å2 / Biso min: 17.91 Å2
Refinement stepCycle: final / Resolution: 2.3→36.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4028 0 47 121 4196
Biso mean--64.72 43.72 -
Num. residues----533
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024132
X-RAY DIFFRACTIONf_angle_d0.5155643
X-RAY DIFFRACTIONf_chiral_restr0.034648
X-RAY DIFFRACTIONf_plane_restr0.004717
X-RAY DIFFRACTIONf_dihedral_angle_d9.0341433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3002-2.33050.39961300.35191054118477
2.3305-2.36240.32491030.33051073117676
2.3624-2.39610.3141270.33671020114778
2.3961-2.43190.40421170.31221099121678
2.4319-2.46990.29181100.2991078118879
2.4699-2.51040.32251300.30081108123880
2.5104-2.55360.33821330.30321135126884
2.5536-2.60010.40181390.28371160129985
2.6001-2.65010.3011190.28821167128685
2.6501-2.70410.29671310.28361226135787
2.7041-2.76290.33161330.27831185131887
2.7629-2.82720.31441450.26751234137990
2.8272-2.89780.28891530.26141249140291
2.8978-2.97620.31611330.27461275140891
2.9762-3.06370.27031450.25841286143194
3.0637-3.16250.28731340.25081318145295
3.1625-3.27550.28381520.24341306145896
3.2755-3.40650.25771460.24431343148996
3.4065-3.56150.2841450.22581325147097
3.5615-3.7490.241770.22151345152297
3.749-3.98370.23491380.20731360149898
3.9837-4.29080.22781590.19811374153399
4.2908-4.72180.23731530.18391373152699
4.7218-5.40320.1991450.19241402154799
5.4032-6.80020.23951830.215213761559100
6.8002-36.50780.22151480.20791437158599

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