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- PDB-4r8c: Crystal Structure of CNG mimicking NaK-ETPP mutant in complex with Rb+ -

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Basic information

Entry
Database: PDB / ID: 4r8c
TitleCrystal Structure of CNG mimicking NaK-ETPP mutant in complex with Rb+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / Alpha helical membrane protein / chimera channel
Function / homology
Function and homology information


potassium channel activity / endomembrane system / identical protein binding / membrane / metal ion binding
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
GLYCINE / RUBIDIUM ION / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionSep 1, 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: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Sep 20, 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 / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_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.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,75320
Polymers21,2532
Non-polymers1,50018
Water48627
1
A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules

A: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,50640
Polymers42,5064
Non-polymers3,00036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area7630 Å2
ΔGint-121 kcal/mol
Surface area14750 Å2
MethodPISA
2
B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules

B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,50640
Polymers42,5064
Non-polymers3,00036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area9370 Å2
ΔGint-148 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.305, 67.305, 84.294
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
11A-201-

RB

21A-202-

RB

31A-203-

RB

41B-201-

RB

51B-202-

RB

61B-203-

RB

71A-312-

HOH

81A-313-

HOH

91B-307-

HOH

DetailsTetrameric channel with pore on 4-fold axis

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Components

#1: Protein Potassium channel protein


Mass: 10626.555 Da / Num. of mol.: 2 / 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-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal growMethod: vapor diffusion, hanging drop
Details: CNG-ETPP(K+) crystals grown in 100mM MES pH 6.5, 60-66% (w/v) MPD, 100mM Glycine, Soaking O.N. in 70% MPD, 10mM DM, 100mM Hepes pH 7.5 and 100mM RbCl, VAPOR DIFFUSION, HANGING DROP
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8156 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8156 Å / Relative weight: 1
ReflectionResolution: 2.5→47.59 Å / Num. all: 6549 / Num. obs: 6549 / % possible obs: 100 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-47.590.0636.11100
2.5-2.640.431.61100

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Processing

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

3k0d


Resolution: 2.5→47.59 Å / σ(F): 1.6 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 290 RANDOM
Rwork0.204 --
obs0.264 6200 -
all-6233 -
Refinement stepCycle: LAST / Resolution: 2.5→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 72 27 1371
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.0118
X-RAY DIFFRACTIONr_angle_refined_deg1.3811

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