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- PDB-5e1a: Structure of KcsA with L24C/R117C mutations -

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Basic information

Entry
Database: PDB / ID: 5e1a
TitleStructure of KcsA with L24C/R117C mutations
Components
  • antibody Fab fragment heavy chain
  • antibody Fab fragment light chain
  • pH-gated potassium channel KcsA
KeywordsMETAL TRANSPORT / KcsA / mutation / protons / potassium channels
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsUpadhyay, V. / Kim, D.M. / Nimigean, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5RO1GM088352 United States
CitationJournal: J.Gen.Physiol. / Year: 2016
Title: Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles.
Authors: Kim, D.M. / Dikiy, I. / Upadhyay, V. / Posson, D.J. / Eliezer, D. / Nimigean, C.M.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 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 / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain
C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1617
Polymers60,0053
Non-polymers1564
Water0
1
A: antibody Fab fragment heavy chain
B: antibody Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)46,8472
Polymers46,8472
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area19940 Å2
MethodPISA
2
C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules

C: pH-gated potassium channel KcsA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,25620
Polymers52,6304
Non-polymers62616
Water0
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
Buried area8120 Å2
ΔGint-80 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.794, 154.794, 74.479
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11C-3001-

K

21C-3002-

K

31C-3003-

K

41C-3004-

K

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Components

#1: Antibody antibody Fab fragment heavy chain


Mass: 23411.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody antibody Fab fragment light chain


Mass: 23435.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein pH-gated potassium channel KcsA / Streptomyces lividans K+ channel / SKC1


Mass: 13157.530 Da / Num. of mol.: 1 / Fragment: UNP residues 4-124 / Mutation: L24C, R117C
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.75 / Details: PEG 400, MES, Magnesium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2015
RadiationMonochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.4→48.95 Å / Num. obs: 12268 / % possible obs: 99.8 % / Redundancy: 13.26 % / Biso Wilson estimate: 150.2 Å2 / Rsym value: 0.15 / Net I/σ(I): 14.16
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 13.52 % / Rmerge(I) obs: 3.3 / Mean I/σ(I) obs: 1.06 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K4C

1k4c


Resolution: 3.4→48.95 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2571 1222 9.97 %
Rwork0.2472 --
obs0.2481 12261 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 4 0 4049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034155
X-RAY DIFFRACTIONf_angle_d0.6435652
X-RAY DIFFRACTIONf_dihedral_angle_d10.71455
X-RAY DIFFRACTIONf_chiral_restr0.023646
X-RAY DIFFRACTIONf_plane_restr0.003718
Refinement TLS params.Method: refined / Origin x: -28.1683 Å / Origin y: 19.9209 Å / Origin z: 31.9759 Å
111213212223313233
T1.2825 Å20.5197 Å20.0319 Å2-1.3187 Å20.1834 Å2--1.1343 Å2
L2.2535 °2-1.0582 °2-1.8262 °2-2.3873 °22.8917 °2--6.0215 °2
S-0.0777 Å °-0.1093 Å °-0.2094 Å °0.3168 Å °-0.2404 Å °0.502 Å °-0.926 Å °-1.5015 Å °0.2549 Å °
Refinement TLS groupSelection details: all

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