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- PDB-3ifx: Crystal structure of the Spin-labeled KcsA mutant V48R1 -

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Basic information

Entry
Database: PDB / ID: 3ifx
TitleCrystal structure of the Spin-labeled KcsA mutant V48R1
ComponentsVoltage-gated potassium channel
KeywordsMEMBRANE PROTEIN / potassium channel / spin-labeled protein / Cell membrane / Ion transport / Ionic channel / Membrane / Transmembrane / Transport / Voltage-gated channel
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-MTN / TETRABUTYLAMMONIUM ION / pH-gated potassium channel KcsA
Similarity search - Component
Biological speciesStreptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / EPR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.56 Å
AuthorsCieslak, J.A. / Focia, P.J. / Gross, A.
CitationJournal: Biochemistry / Year: 2010
Title: Electron Spin-Echo Envelope Modulation (ESEEM) Reveals Water and Phosphate Interactions with the KcsA Potassium Channel
Authors: Cieslak, J.A. / Focia, P.J. / Gross, A.
History
DepositionJul 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Advisory / Non-polymer description / Refinement description
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,14811
Polymers55,7704
Non-polymers1,3787
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-71.8 kcal/mol
Surface area17840 Å2
MethodPISA
2
A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules

A: Voltage-gated potassium channel
B: Voltage-gated potassium channel
C: Voltage-gated potassium channel
D: Voltage-gated potassium channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,29522
Polymers111,5398
Non-polymers2,75614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15600 Å2
ΔGint-157.6 kcal/mol
Surface area33960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.970, 76.630, 112.970
Angle α, β, γ (deg.)90.00, 125.83, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE QUATERNARY STRUCTURE DEFINED IN REMARK 350 AS BIOMOLECULE 1 IS THE CORRECT PHYSIOLOGICAL TETRAMER THAT FORMS AN ASYMMETRIC UNIT. THE QUATERNARY STRUCTURE DEFINED IN REMARK 350 AS BIOMOLECULE 2 IS INCORRECT AS THE OCTAMERIC STRUCTURE IS A CONSEQUENCE OF CRYSTAL PACKING AND FORMATION OF THE CONTENTS OF THE UNIT CELL.

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Components

#1: Protein
Voltage-gated potassium channel /


Mass: 13942.380 Da / Num. of mol.: 4 / Fragment: Pore domain: UNP residues 1-124 / Mutation: V48C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lividans (bacteria) / Gene: kcsA, skc1 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A334
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18NO3S2
#4: Chemical ChemComp-TBA / TETRABUTYLAMMONIUM ION / Tetrabutylammonium


Mass: 242.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H36N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
EPR1

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Sample preparation

CrystalDensity Matthews: 4.28 Å3/Da / Density % sol: 71.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM CaCl2, 150 mM KCl, 100 mM HEPES, 19-49% PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 15, 2008
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.56→50 Å / Num. all: 7946 / Num. obs: 7898 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 4
Reflection shellResolution: 3.56→3.65 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.0421 / Mean I/σ(I) obs: 1.7 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
REFMAC5.5.0051refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BL8

1bl8


Resolution: 3.56→24.84 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.897 / SU B: 66.443 / SU ML: 0.512 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.721 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30218 409 4.9 %RANDOM
Rwork0.27109 ---
all0.27267 7898 --
obs0.27267 7898 75.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 110.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.67 Å2
2---0.12 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 3.56→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 49 3 2795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0550.0222914
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9644018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.335388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9721.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg26.17715353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.683157
X-RAY DIFFRACTIONr_chiral_restr0.0860.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212074
X-RAY DIFFRACTIONr_mcbond_it0.8181.5107
X-RAY DIFFRACTIONr_mcangle_it1.5112165
X-RAY DIFFRACTIONr_scbond_it0.844341
X-RAY DIFFRACTIONr_scangle_it1.6814.540
LS refinement shellResolution: 3.56→3.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 5 -
Rwork0.354 66 -
obs--8.78 %
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
136.532929.931921.6098
226.096716.081425.3794
313.41326.824630.2369
423.451940.586126.4115
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B23 - 34
2X-RAY DIFFRACTION1B35 - 56
3X-RAY DIFFRACTION1B57 - 67
4X-RAY DIFFRACTION1B68 - 78
5X-RAY DIFFRACTION1B79 - 89
6X-RAY DIFFRACTION1B90 - 112
7X-RAY DIFFRACTION1B113 - 119
8X-RAY DIFFRACTION2C23 - 36
9X-RAY DIFFRACTION2C37 - 47
10X-RAY DIFFRACTION2C48 - 60
11X-RAY DIFFRACTION2C61 - 65
12X-RAY DIFFRACTION2C66 - 82
13X-RAY DIFFRACTION2C83 - 92
14X-RAY DIFFRACTION2C93 - 110
15X-RAY DIFFRACTION2C111 - 119
16X-RAY DIFFRACTION3D23 - 34
17X-RAY DIFFRACTION3D35 - 56
18X-RAY DIFFRACTION3D57 - 67
19X-RAY DIFFRACTION3D68 - 78
20X-RAY DIFFRACTION3D79 - 89
21X-RAY DIFFRACTION3D90 - 112
22X-RAY DIFFRACTION3D113 - 119
23X-RAY DIFFRACTION4A23 - 36
24X-RAY DIFFRACTION4A37 - 47
25X-RAY DIFFRACTION4A48 - 60
26X-RAY DIFFRACTION4A61 - 65
27X-RAY DIFFRACTION4A66 - 82
28X-RAY DIFFRACTION4A83 - 92
29X-RAY DIFFRACTION4A93 - 110
30X-RAY DIFFRACTION4A111 - 119

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