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- PDB-3t2m: Crystal Structure of NaK Channel N68D Mutant -

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Basic information

Entry
Database: PDB / ID: 3t2m
TitleCrystal Structure of NaK Channel N68D Mutant
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / Ion Channel
Function / homology
Function and homology information


potassium channel activity / 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
: / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.953 Å
AuthorsSauer, D.B. / Zeng, W. / Raghunathan, S. / Jiang, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Protein interactions central to stabilizing the K+ channel selectivity filter in a four-sited configuration for selective K+ permeation.
Authors: Sauer, D.B. / Zeng, W. / Raghunathan, S. / Jiang, Y.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Feb 28, 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_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_atom_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_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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)21,7219
Polymers21,4472
Non-polymers2747
Water1629
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)43,36416
Polymers42,8944
Non-polymers46912
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 area6850 Å2
ΔGint-57 kcal/mol
Surface area18090 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)43,52020
Polymers42,8944
Non-polymers62616
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 area6670 Å2
ΔGint-54 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.088, 68.088, 89.081
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-1-

K

21A-5-

K

31A-7-

K

41B-2-

K

51B-3-

K

61B-4-

K

71B-6-

K

81A-2-

HOH

91B-1-

HOH

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Components

#1: Protein Potassium channel protein


Mass: 10723.587 Da / Num. of mol.: 2 / Mutation: N68D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / DSM 31 / Gene: BC_0669 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q81HW2
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 70% MPD, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9785736 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785736 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 14516 / Observed criterion σ(I): 1.17
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allDiffraction-ID% possible all
1.95-1.984.9639184.5
1.98-2.025.4640189.1
2.02-2.065.6702194.2
2.06-2.16712197.7
2.1-2.156.5738199.7
2.15-2.27.17471100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.953→34.044 Å / σ(F): 1.36 / Phase error: 37.75 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 731 5.04 %Random
Rwork0.1908 ---
obs0.2039 14512 98.12 %-
all-14516 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.3 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.6001 Å2-0 Å20 Å2
2---3.6001 Å2-0 Å2
3---7.2003 Å2
Refinement stepCycle: LAST / Resolution: 1.953→34.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 7 9 1493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051511
X-RAY DIFFRACTIONf_angle_d0.7132060
X-RAY DIFFRACTIONf_dihedral_angle_d11.225520
X-RAY DIFFRACTIONf_chiral_restr0.055259
X-RAY DIFFRACTIONf_plane_restr0.002250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.953-2.10460.3091340.27672551X-RAY DIFFRACTION87
2.1046-2.31610.28111620.25722766X-RAY DIFFRACTION94
2.3161-2.65080.23021400.22522804X-RAY DIFFRACTION95
2.6508-3.33770.22361450.20392796X-RAY DIFFRACTION95
3.3377-21.53260.23451480.1742838X-RAY DIFFRACTION95
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)
10.20780.0739-0.06750.5702-0.13730.39210.00170.0076-0.22410.1043-0.05810.12650.172-0.04660.07310.2028-0.0220.04890.21290.03330.2568-1.1169-12.97324.636
20.20120.0487-0.15890.4315-0.12140.1311-0.1165-0.2251-0.07780.20690.10260.2666-0.2226-0.21260.02450.32140.05990.07320.18620.05390.2267-11.2849-6.8576-22.0093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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