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- PDB-3k04: Crystal Structure of CNG mimicking NaK mutant, NaK-DTPP, Na+ complex -

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Basic information

Entry
Database: PDB / ID: 3k04
TitleCrystal Structure of CNG mimicking NaK mutant, NaK-DTPP, Na+ complex
ComponentsPotassium channel protein NaK
KeywordsTRANSPORT PROTEIN / NaK-DTPP / DTPP / NaK / CNG mimicking / CNG channel selectivity filter / NaK-mutant / Ionic channel
Function / homology
Function and homology information


stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / membrane / identical protein binding / 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
Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsJiang, Y. / Derebe, M.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural studies of ion permeation and Ca2+ blockage of a bacterial channel mimicking the cyclic nucleotide-gated channel pore.
Authors: Derebe, M.G. / Zeng, W. / Li, Y. / Alam, A. / Jiang, Y.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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 / _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_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_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 NaK
B: Potassium channel protein NaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,11816
Polymers21,2252
Non-polymers89314
Water2,648147
1
A: Potassium channel protein NaK
hetero molecules

A: Potassium channel protein NaK
hetero molecules

A: Potassium channel protein NaK
hetero molecules

A: Potassium channel protein NaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,89344
Polymers42,4504
Non-polymers2,44340
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area13350 Å2
ΔGint-365 kcal/mol
Surface area16060 Å2
MethodPISA
2
B: Potassium channel protein NaK
hetero molecules

B: Potassium channel protein NaK
hetero molecules

B: Potassium channel protein NaK
hetero molecules

B: Potassium channel protein NaK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,57920
Polymers42,4504
Non-polymers1,12916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area10650 Å2
ΔGint-223 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.840, 67.840, 89.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-2-

NA

21A-4-

NA

31A-5-

NA

41A-6-

NA

51A-7-

NA

61A-8-

NA

71B-1-

NA

81B-3-

NA

91A-1-

HOH

101B-117-

HOH

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Components

#1: Protein Potassium channel protein NaK /


Mass: 10612.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: BC_0669 / Production host: Escherichia coli (E. coli) / References: UniProt: Q81HW2
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAT THE REGION, THREE RESIDUES TPP WERE USED TO REPLACE THE FOUR RESIDUES GNFS IN THE UNP SEQUENCE REFERENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: MPD, NaCl, pH 6.5-8.5, vapor diffusion, temperature 293K
PH range: 6.5-8.5

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.58 Å / Num. obs: 27690

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 1.58 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.235 1378 5 %
Rwork0.218 --
obs-27606 99.7 %
Solvent computationBsol: 115.425 Å2
Displacement parametersBiso max: 88.57 Å2 / Biso mean: 39.022 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Highest resolution: 1.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1445 0 56 147 1648
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.451
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4MPD.par

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