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- PDB-4pdm: Crystal Structure of K+ selective NaK mutant in rubidium -

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Basic information

Entry
Database: PDB / ID: 4pdm
TitleCrystal Structure of K+ selective NaK mutant in rubidium
ComponentsPotassium channel protein
KeywordsTRANSPORT PROTEIN / Bacillus cereus / Binding Sites / Electrophysiology / Ions / Potassium / Potassium Channels / Sodium / rubidium / blockage
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
RUBIDIUM ION / Potassium channel protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLam, 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_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_oper_list.symmetry_operation
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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_initial_refinement_model / 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_seq_id / _struct_conn.ptnr2_label_asym_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)22,41111
Polymers21,5432
Non-polymers8679
Water1,42379
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)44,58520
Polymers43,0874
Non-polymers1,49816
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 area9080 Å2
ΔGint-146 kcal/mol
Surface area17060 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)45,05824
Polymers43,0874
Non-polymers1,97120
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 area11700 Å2
ΔGint-231 kcal/mol
Surface area16810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.011, 68.011, 89.346
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-201-

RB

21A-202-

RB

31A-203-

RB

41B-201-

RB

51B-202-

RB

61B-203-

RB

71A-325-

HOH

81A-327-

HOH

91A-333-

HOH

101B-311-

HOH

111B-324-

HOH

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Components

#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
#2: Chemical
ChemComp-RB / RUBIDIUM ION


Mass: 85.468 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Rb
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 65%MPD, 100mM KCl, 100mM MES, 4mM n-Decyl-beta-D-Maltoside
PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / 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: 1.58→50 Å / Num. obs: 27782 / % possible obs: 99.86 % / Redundancy: 7.4 % / Rsym value: 0.049 / Net I/σ(I): 48.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OUF

3ouf


Resolution: 1.58→34.005 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1395 5.02 %Random selection
Rwork0.2043 ---
obs0.2057 27778 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→34.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1485 0 30 79 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071542
X-RAY DIFFRACTIONf_angle_d1.0652104
X-RAY DIFFRACTIONf_dihedral_angle_d13.699528
X-RAY DIFFRACTIONf_chiral_restr0.042262
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.63650.31071490.27472619X-RAY DIFFRACTION100
1.6365-1.7020.29591190.24992631X-RAY DIFFRACTION100
1.702-1.77940.28251500.25422640X-RAY DIFFRACTION100
1.7794-1.87330.29661160.23092677X-RAY DIFFRACTION100
1.8733-1.99060.23591580.22212609X-RAY DIFFRACTION100
1.9906-2.14430.22861280.20322634X-RAY DIFFRACTION100
2.1443-2.360.22961500.19862629X-RAY DIFFRACTION100
2.36-2.70140.20061510.19162627X-RAY DIFFRACTION100
2.7014-3.4030.25591350.19772663X-RAY DIFFRACTION100
3.403-34.01340.21991390.19752654X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -6.2467 Å / Origin y: -9.458 Å / Origin z: 0.5023 Å
111213212223313233
T0.1018 Å2-0.0066 Å20.0511 Å2-0.1204 Å20.0214 Å2--0.1265 Å2
L-0.0954 °20.0181 °2-0.1125 °2-0.3138 °20.0143 °2--0.1198 °2
S0.0017 Å °-0.006 Å °0.0525 Å °0.0114 Å °-0.0442 Å °-0.0281 Å °0.1059 Å °-0.012 Å °-0 Å °
Refinement TLS groupSelection details: all

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