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- PDB-4pdl: Structure of K+ selective NaK mutant in caesium -

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Basic information

Entry
Database: PDB / ID: 4pdl
TitleStructure of K+ selective NaK mutant in caesium
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / Binding Sites / Electrophysiology / Ions / Ligands / Mutation / Potassium / Potassium Channels / Sodium / Caesium / membrane protein
Function / homology
Function and homology information


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
: / HEXANE / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsLam, Y. / Zeng, W. / Sauer, D.B. / Jiang, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079179 United States
Welch FoundationGrant I-1578 United States
CitationJournal: To Be Published
Title: High Resolution Structural Views of Rubidium, Cesium and Barium Binding within a Potassium Selective Channel Filter
Authors: Lam, Y. / Zeng, W. / Sauer, D.B. / Jiang, Y.
History
DepositionApr 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 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_struct_conn_angle / refine_hist / struct_conn
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_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_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_symmetry

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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)22,75813
Polymers21,5432
Non-polymers1,21411
Water88349
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)46,06432
Polymers43,0874
Non-polymers2,97728
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 area13880 Å2
ΔGint-610 kcal/mol
Surface area15280 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)44,96720
Polymers43,0874
Non-polymers1,88116
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 area11290 Å2
ΔGint-244 kcal/mol
Surface area16940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.106, 68.106, 89.593
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-202-

CS

21A-203-

CS

31A-204-

NA

41B-201-

CS

51B-202-

CS

61A-315-

HOH

71A-317-

HOH

81B-305-

HOH

91B-316-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Potassium channel protein /


Mass: 10771.673 Da / Num. of mol.: 2 / Fragment: UNP residues 20-110 / Mutation: D66Y,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

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Non-polymers , 5 types, 60 molecules

#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-HEX / HEXANE / Hexane


Mass: 86.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 48.99 % / Description: Thin square plates.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 65% MPD, 100mM CsCl, 100mM MES, 4mM DM / PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22437 / % possible obs: 99.86 % / Redundancy: 7.4 % / Rsym value: 0.042 / Net I/σ(I): 49.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 1.7→34.053 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 2269 5.13 %Random selection
Rwork0.207 ---
obs0.2085 44200 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→34.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 42 49 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081552
X-RAY DIFFRACTIONf_angle_d1.0822112
X-RAY DIFFRACTIONf_dihedral_angle_d12.526534
X-RAY DIFFRACTIONf_chiral_restr0.045262
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73750.31611350.30282623X-RAY DIFFRACTION99
1.7375-1.77790.29771220.28522654X-RAY DIFFRACTION100
1.7779-1.82240.28341520.27262612X-RAY DIFFRACTION100
1.8224-1.87160.28581300.25032613X-RAY DIFFRACTION100
1.8716-1.92670.28261470.25342630X-RAY DIFFRACTION100
1.9267-1.98890.33481140.2422642X-RAY DIFFRACTION100
1.9889-2.060.25521430.2292655X-RAY DIFFRACTION100
2.06-2.14240.26781660.23442560X-RAY DIFFRACTION100
2.1424-2.23990.24251690.22242618X-RAY DIFFRACTION100
2.2399-2.3580.23561660.20382604X-RAY DIFFRACTION100
2.358-2.50570.21831480.20592595X-RAY DIFFRACTION100
2.5057-2.69910.2121890.19482671X-RAY DIFFRACTION100
2.6991-2.97060.21381590.18992627X-RAY DIFFRACTION100
2.9706-3.40010.23091270.18462641X-RAY DIFFRACTION100
3.4001-4.28240.18211570.18392599X-RAY DIFFRACTION100
4.2824-34.05980.26131450.20972587X-RAY DIFFRACTION98

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