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- PDB-6sx7: Crystal Structure of the Voltage-Gated Sodium Channel NavMs (F208... -

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Basic information

Entry
Database: PDB / ID: 6sx7
TitleCrystal Structure of the Voltage-Gated Sodium Channel NavMs (F208L) (2.2 Angstrom resolution)
ComponentsIon transport proteinIon transporter
KeywordsMETAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein.
Function / homologyVoltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / plasma membrane / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE / Ion transport protein
Function and homology information
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSula, A. / Hollingworth, D. / Wallace, B.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/L006790, BB/N012763 and BB/R001294 United Kingdom
CitationJournal: Mol.Cell / Year: 2021
Title: A tamoxifen receptor within a voltage-gated sodium channel.
Authors: Sula, A. / Hollingworth, D. / Ng, L.C.T. / Larmore, M. / DeCaen, P.G. / Wallace, B.A.
History
DepositionSep 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 31, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 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)32,7098
Polymers31,1861
Non-polymers1,5237
Water1,24369
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)130,83432
Polymers124,7434
Non-polymers6,09128
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 area22970 Å2
ΔGint-174 kcal/mol
Surface area52710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.004, 109.004, 208.827
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

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Protein , 1 types, 1 molecules A

#1: Protein Ion transport protein / Ion transporter


Mass: 31185.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Production host: Escherichia coli (E. coli) / References: UniProt: A0L5S6

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Non-polymers , 5 types, 76 molecules

#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 / Polyethylene glycol


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Chemical ChemComp-ME2 / 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M NaCl, 0.1 M Li2SO4, 0.1 M sodium citrate buffer, pH 5, 300% v/v polyethylene glycol (PEG) 300
Temp details: 4 degrees celcius

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→27.25 Å / Num. obs: 22217 / % possible obs: 100 % / Redundancy: 16.4 % / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 2.5→2.6 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2459 / CC1/2: 0.958

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVX

5hvx


Resolution: 2.5→27.25 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.863 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.194 / SU Rfree Cruickshank DPI: 0.195
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1141 5.14 %RANDOM
Rwork0.232 ---
obs0.232 22192 100 %-
Displacement parametersBiso max: 246.12 Å2 / Biso mean: 88.1 Å2 / Biso min: 35.69 Å2
Baniso -1Baniso -2Baniso -3
1--13.9824 Å20 Å20 Å2
2---13.9824 Å20 Å2
3---27.9648 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: final / Resolution: 2.5→27.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2085 0 66 69 2220
Biso mean--86.97 79.13 -
Num. residues----264
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d783SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes351HARMONIC5
X-RAY DIFFRACTIONt_it2185HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion294SEMIHARMONIC5
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_contact2606SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2185HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2948HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion18.93
LS refinement shellResolution: 2.5→2.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2109 22 4.95 %
Rwork0.2194 422 -
all0.219 444 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 47.5601 Å / Origin y: 72.2962 Å / Origin z: 30.892 Å
111213212223313233
T-0.0396 Å20.0852 Å20.0145 Å2--0.1513 Å2-0.0767 Å2---0.1721 Å2
L0.9126 °2-0.1447 °2-0.1732 °2-0.5991 °20.228 °2--2.0562 °2
S-0.0442 Å °-0.2462 Å °0.2099 Å °0.1955 Å °0.0068 Å °0.054 Å °-0.5442 Å °-0.2623 Å °0.0374 Å °
Refinement TLS groupSelection details: { A|* }

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