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- PDB-6dz1: Studies of Ion Transport in K+ Channels -

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Basic information

Entry
Database: PDB / ID: 6dz1
TitleStudies of Ion Transport in K+ Channels
ComponentsPotassium channel protein
KeywordsMEMBRANE PROTEIN / K ion transport channel
Function / homologyHelix Hairpins - #70 / Potassium channel domain / Ion channel / membrane => GO:0016020 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / : / Potassium channel protein
Function and homology information
Biological speciesBacillus cereus BDRD-Cer4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.26 Å
AuthorsLangan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Wagner, A. / Duman, R. / El Omari, K. / Afonine, P.V. / Coates, L.
CitationJournal: Nat Commun / Year: 2018
Title: Anomalous X-ray diffraction studies of ion transport in K+channels.
Authors: Langan, P.S. / Vandavasi, V.G. / Weiss, K.L. / Afonine, P.V. / El Omari, K. / Duman, R. / Wagner, A. / Coates, L.
History
DepositionJul 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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)21,88415
Polymers21,1392
Non-polymers74613
Water46826
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)43,84928
Polymers42,2784
Non-polymers1,57124
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 area9710 Å2
ΔGint-164 kcal/mol
Surface area18050 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)43,68932
Polymers42,2784
Non-polymers1,41128
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 area9570 Å2
ΔGint-97 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.070, 68.070, 89.380
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-

K

21A-202-

K

31A-203-

K

41A-204-

K

51B-201-

K

61B-202-

K

71B-203-

K

81B-204-

K

91A-312-

HOH

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Components

#1: Protein Potassium channel protein


Mass: 10569.399 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus BDRD-Cer4 (bacteria) / Gene: bcere0015_5640 / Production host: Escherichia coli (E. coli) / References: UniProt: C2SWC7
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: K
#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.: 26 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: Prepared by mixing equal volumes of protein solution in buffer (20mM Tris:HCl pH 7.8, 100mM KCl, and 4mM Anagrade DM) with well solution (72.5%MPD, 100mM KCl, and 100mM MES pH 6)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.35 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 3.35 Å / Relative weight: 1
ReflectionResolution: 2.26→54.15 Å / Num. obs: 18417 / % possible obs: 97.8 % / Redundancy: 8.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.019 / Net I/σ(I): 33.4
Reflection shellResolution: 2.26→2.33 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 10.7 / CC1/2: 0.987 / Rpim(I) all: 0.082 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.26→54.154 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.58 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 920 5 %
Rwork0.1782 --
obs0.1799 18417 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→54.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 34 26 1542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141538
X-RAY DIFFRACTIONf_angle_d1.0872096
X-RAY DIFFRACTIONf_dihedral_angle_d13.278528
X-RAY DIFFRACTIONf_chiral_restr0.076261
X-RAY DIFFRACTIONf_plane_restr0.007248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2602-2.37940.22911050.17282412X-RAY DIFFRACTION95
2.3794-2.52840.23161520.16822442X-RAY DIFFRACTION96
2.5284-2.72360.15781270.14732485X-RAY DIFFRACTION97
2.7236-2.99770.19721270.16442503X-RAY DIFFRACTION99
2.9977-3.43140.23261160.17012575X-RAY DIFFRACTION100
3.4314-4.3230.18861290.17442554X-RAY DIFFRACTION100
4.323-54.1690.22881640.20152526X-RAY DIFFRACTION100

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