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- PDB-4ro2: Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized... -

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Basic information

Entry
Database: PDB / ID: 4ro2
TitleCrystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized with Methylammonium
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / Alpha helical membrane protein / ion channel
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
methylammonium ion / GLYCINE / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionOct 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)45,14538
Polymers42,5064
Non-polymers2,63934
Water91951
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)45,59544
Polymers42,5064
Non-polymers3,08940
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area8630 Å2
ΔGint-100 kcal/mol
Surface area18160 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)44,69532
Polymers42,5064
Non-polymers2,18828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area6670 Å2
ΔGint-64 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.696, 91.045, 67.622
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
11A-201-

3P8

21A-201-

3P8

31C-201-

3P8

41C-201-

3P8

51A-302-

HOH

61C-302-

HOH

71C-303-

HOH

81C-304-

HOH

DetailsThe asymmetric unit is composed by two dimers. By 2-fold symmetry two tetramers are generated by each dimers.

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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 / Plasmid: pQE60-NaK2CNG-ETPP / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q81HW2
#2: Chemical ChemComp-3P8 / methylammonium ion / methanaminium


Mass: 32.065 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH6N
#3: Chemical...
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES pH 6.5, 25mM Glycine, 40-44% MPD, 100mM MACl, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.542 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 12, 2014
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.7→47.84 Å / Num. all: 11995 / Num. obs: 11995 / % possible obs: 100 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.7-47.845.20.09611.71100
2.7-2.8550.3933.91100

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Processing

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

3k0d


Resolution: 2.7→45.52 Å / σ(F): 1.7 / Stereochemistry target values: Engh & Huber / Details: TWIN REFINEMENT with REFMAC5
RfactorNum. reflectionSelection details
Rfree0.283 514 RANDOM
Rwork0.248 --
obs0.2613 10025 -
all-10698 -
Refinement stepCycle: LAST / Resolution: 2.7→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 176 51 2747
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.5136
X-RAY DIFFRACTIONr_bond_refined_d0.0108

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