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- PDB-4r50: Crystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized... -

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Basic information

Entry
Database: PDB / ID: 4r50
TitleCrystal Structure of CNG mimicking NaK-ETPP mutant cocrystallized with Li+
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / Alpha helical membrane protein / chimera 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
GLYCINE / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 20, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: Potassium channel protein
B: Potassium channel protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8229
Polymers21,2532
Non-polymers5697
Water86548
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

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)87,28736
Polymers85,0128
Non-polymers2,27428
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_664-x+1,-y+1,z-11
crystal symmetry operation3_654-y+1,x,z-11
crystal symmetry operation4_564y,-x+1,z-11
Buried area15630 Å2
ΔGint-157 kcal/mol
Surface area33030 Å2
MethodPISA
2
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)43,88020
Polymers42,5064
Non-polymers1,37316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6540 Å2
ΔGint-59 kcal/mol
Surface area16110 Å2
MethodPISA
3
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)43,40716
Polymers42,5064
Non-polymers90112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area8150 Å2
ΔGint-82 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.570, 67.570, 88.530
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-301-

HOH

21A-316-

HOH

31A-317-

HOH

41A-323-

HOH

51A-324-

HOH

61A-325-

HOH

71B-301-

HOH

81B-302-

HOH

91B-303-

HOH

101B-312-

HOH

111B-320-

HOH

121B-321-

HOH

131B-322-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 22 - 109 / Label seq-ID: 5 - 92

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsTetrameric channel with filter on the 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 / Plasmid: pQE60 / Cell line (production host): XL1-Blue / Production host: Escherichia coli (E. coli) / References: UniProt: Q81HW2
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE AUTHORS STATE THAT THE LITHIUM ION COULD BE AT THE BRIDGE OF TWO WATER MOLECULES IN THE CENTRAL ...THE AUTHORS STATE THAT THE LITHIUM ION COULD BE AT THE BRIDGE OF TWO WATER MOLECULES IN THE CENTRAL CAVITY OF THE K-CHANNELS. SINCE IT HAS ONLY 3 ELECTRONS THE RESOLUTION IS NOT SUFFICIENT TO DETERMINE ITS POSITION WITH A HIGH DEGREE OF RELIABILITY. THEREFORE, ONLY THE TWO WATER MOLECULES WERE INCLUDED IN THE COORDINATES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 40-70% MPD, 20-100mM Glycine, pH 6.5 - 7.5, VAPOR DIFFUSION, HANGING DROP
PH range: 6.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 8, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -H,K,-L / Fraction: 0.4761
ReflectionResolution: 2.85→33.81 Å / Num. obs: 4692 / % possible obs: 83 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.85-33.780.1485.1199.9
2.85-30.3811.91100

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Processing

Software
NameVersionClassification
ElettraXRD1 softwaredata collection
MOLREPphasing
REFMAC5.7.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K0D: chain A without filter and solvent

3k0d


Resolution: 2.85→33.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 17.387 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R Free: 0.319
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18295 480 10.2 %RANDOM
Rwork0.12505 ---
obs0.13103 4212 99.85 %-
all-4692 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.85→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 38 48 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021441
X-RAY DIFFRACTIONr_bond_other_d0.0040.021394
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9991969
X-RAY DIFFRACTIONr_angle_other_deg1.03333187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0195181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9822.95544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59815202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.98153
X-RAY DIFFRACTIONr_chiral_restr0.0770.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211577
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02312
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_it1.0192.047748
X-RAY DIFFRACTIONr_mcbond_other1.032.078729
X-RAY DIFFRACTIONr_mcangle_it1.6783.089921
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8312.074693
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 4385 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 35 -
Rwork0.146 304 -
obs--99.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.61490.9886-0.37823.20760.58790.207-0.02810.47410.0201-0.2867-0.04960.3428-0.0759-0.11290.07770.14820.0115-0.02680.2117-0.02130.039220.74230.98321.817
22.8765-0.48440.46561.45420.31911.68790.00280.0467-0.1405-0.1398-0.04890.12670.2064-0.07750.04610.1818-0.0428-0.00030.1926-0.04420.02326.91522.49466.646
30.85680.443-0.1010.2462-0.05970.01580.0722-0.47820.07420.0621-0.0906-0.0153-0.0061-0.01020.01840.55220.2995-0.22561.6366-0.44370.256723.56930.9451.556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 110
2X-RAY DIFFRACTION2B20 - 113
3X-RAY DIFFRACTION3A202 - 204
4X-RAY DIFFRACTION3B201 - 203

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