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- PDB-4r7c: Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized... -

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Basic information

Entry
Database: PDB / ID: 4r7c
TitleCrystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized with DiMethylammonium
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / ALPHA-HELICAL membrane protein / NaK-chimera channel in complex with DiMA+
Function / homology
Function and homology information


potassium channel activity / metal ion binding / identical protein binding / membrane
Similarity search - Function
Two pore domain potassium channel / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DIMETHYLAMINE / GLYCINE / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe March, M. / Napolitano, L.M.R. / Onesti, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels.
Authors: Napolitano, L.M. / Bisha, I. / De March, M. / Marchesi, A. / Arcangeletti, M. / Demitri, N. / Mazzolini, M. / Rodriguez, A. / Magistrato, A. / Onesti, S. / Laio, A. / Torre, V.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.3Sep 20, 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 / 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 / _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: Potassium channel protein
B: Potassium channel protein
C: Potassium channel protein
D: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,87467
Polymers42,5064
Non-polymers4,36863
Water1,24369
1
A: Potassium channel protein
B: Potassium channel protein
hetero molecules

A: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00582
Polymers42,5064
Non-polymers5,49978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area7400 Å2
ΔGint-63 kcal/mol
Surface area19350 Å2
MethodPISA
2
C: Potassium channel protein
D: Potassium channel protein
hetero molecules

C: Potassium channel protein
D: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,74252
Polymers42,5064
Non-polymers3,23648
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area6450 Å2
ΔGint-56 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.891, 67.680, 67.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-201-

DMN

21C-201-

DMN

31B-301-

HOH

41B-303-

HOH

51B-305-

HOH

61C-304-

HOH

71C-306-

HOH

81C-307-

HOH

91C-325-

HOH

101C-326-

HOH

DetailsThe biological tetramer is assembled by a crystallographic 2-fold axis which relates two dimers together. The pore of the tetrameric channel is coincident with the 2-fold crystallographic axis.

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Components

#1: Protein
Potassium channel protein


Mass: 10626.555 Da / Num. of mol.: 4 / Fragment: residues 20-110 / Mutation: D66E, G67T, N68P, F69P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_0669 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q81HW2
#2: Chemical...
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical...
ChemComp-DMN / DIMETHYLAMINE


Mass: 45.084 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H7N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal growpH: 6.5
Details: CNG-ETPP(DiMA+) cocrystals grown in 40-44% MPD, 100mM MES pH6.5 and 20-25 mM Glycine, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 6, 2014
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→47.84 Å / Num. obs: 18763 / % possible obs: 99.6 % / Observed criterion σ(I): 2.1
Reflection shellResolution: 2.3→47.84 Å / Rmerge(I) obs: 0.071 / Mean I/σ(I) obs: 4.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ElettraXRD1 softwaredata collection
MOLREPphasing
REFMAC5.7.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K0D

3k0d


Resolution: 2.3→47.84 Å / σ(F): 2.1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 884 RANDOM
Rwork0.207 --
obs0.266 17682 -
all-17816 -
Refinement stepCycle: LAST / Resolution: 2.3→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 292 69 3021
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded

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