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- PDB-6yz2: Full length Open-form Sodium Channel NavMs F208L -

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Basic information

Entry
Database: PDB / ID: 6yz2
TitleFull length Open-form Sodium Channel NavMs F208L
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein.
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / membrane depolarization during action potential / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / Ion transport protein
Function and homology information
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSula, A. / Sait, L.G. / Hollingworth, D. / Wallace, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L006790, BB/N012763 and BB/R001294 United Kingdom
CitationJournal: Elife / Year: 2020
Title: Cannabidiol interactions with voltage-gated sodium channels.
Authors: Sait, L.G. / Sula, A. / Ghovanloo, M.R. / Hollingworth, D. / Ruben, P.C. / Wallace, B.A.
History
DepositionMay 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5979
Polymers31,1291
Non-polymers2,4688
Water1,67593
1
A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules

A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,38636
Polymers124,5154
Non-polymers9,87232
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 area23330 Å2
ΔGint-265 kcal/mol
Surface area50960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.940, 108.940, 209.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-301-

NA

21A-302-

NA

31A-303-

NA

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Components

#1: Protein Ion transport protein


Mass: 31128.680 Da / Num. of mol.: 1 / Mutation: F210L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Gene: Mmc1_0798 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L5S6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37NO7 / Comment: detergent*YM
#4: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M lithium sulphate, 0.1M HEPES, pH 7, and 40% v/v PEG200.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.2→104.68 Å / Num. obs: 32388 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2771 / CC1/2: 0.953

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hvx

5hvx


Resolution: 2.2→104.68 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.887 / SU R Cruickshank DPI: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.164 / SU Rfree Blow DPI: 0.152 / SU Rfree Cruickshank DPI: 0.152
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1571 4.85 %RANDOM
Rwork0.2428 ---
obs0.2438 32388 100 %-
Displacement parametersBiso max: 179.42 Å2 / Biso mean: 76.37 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--11.4588 Å20 Å20 Å2
2---11.4588 Å20 Å2
3---22.9176 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.2→104.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 75 93 2198
Biso mean--85.57 80.43 -
Num. residues----256
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d770SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes342HARMONIC5
X-RAY DIFFRACTIONt_it2149HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion290SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1836SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2149HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg2894HARMONIC20.82
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion16.66
LS refinement shellResolution: 2.2→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.189 28 4.32 %
Rwork0.2214 620 -
all0.2201 648 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 47.5502 Å / Origin y: 71.8823 Å / Origin z: 31.5119 Å
111213212223313233
T0.1001 Å20.0574 Å2-0.0166 Å2--0.0091 Å2-0.0503 Å2--0.0024 Å2
L0.408 °2-0.078 °2-0.1651 °2-0 °2-0.0261 °2--1.0568 °2
S-0.0321 Å °-0.1056 Å °0.0183 Å °0.0548 Å °0.0031 Å °-0.0418 Å °-0.3899 Å °-0.048 Å °0.029 Å °
Refinement TLS groupSelection details: { A|* }

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