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- PDB-6sx5: Full length Mutant Open-form Sodium Channel NavMs -

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Basic information

Entry
Database: PDB / ID: 6sx5
TitleFull length Mutant Open-form Sodium Channel NavMs
ComponentsIon transport protein
KeywordsMETAL TRANSPORT / Voltage Gated Sodium Channel / Membrane protein.
Function / homology
Function and homology information


voltage-gated sodium channel complex / voltage-gated sodium channel activity
Similarity search - Function
Voltage-gated potassium channels. Chain C / Voltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Ion transport domain / Ion transport protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Ion transport protein
Similarity search - Component
Biological speciesMagnetococcus marinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)34,58011
Polymers31,1861
Non-polymers3,39410
Water1,62190
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)138,31944
Polymers124,7434
Non-polymers13,57640
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 area27460 Å2
ΔGint-300 kcal/mol
Surface area53460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.133, 109.133, 209.031
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: 31185.730 Da / Num. of mol.: 1 / Mutation: F208L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus (strain ATCC BAA-1437 / JCM 17883 / MC-1) (bacteria)
Strain: ATCC BAA-1437 / JCM 17883 / MC-1 / 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.: 3 / 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.: 4 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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

CrystalDensity Matthews: 5.22 Å3/Da / Density % sol: 76.45 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 0.05 M NaCl, 0.1 M MES buffer, pH 6.5, 37.8% v/v polyethylene glycol (PEG) 400 and 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9688 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.2→28.8 Å / Num. obs: 32440 / % possible obs: 100 % / Redundancy: 19 % / Biso Wilson estimate: 40.88 Å2 / CC1/2: 0.996 / Net I/σ(I): 14
Reflection shellResolution: 2.2→2.27 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2774 / CC1/2: 0.969 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVX

5hvx


Resolution: 2.2→28.8 Å / Cor.coef. Fo:Fc: 0.895 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.152 / SU Rfree Blow DPI: 0.144 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1618 4.99 %RANDOM
Rwork0.22 ---
obs0.222 32421 100 %-
Displacement parametersBiso max: 279.4 Å2 / Biso mean: 78.06 Å2 / Biso min: 22.46 Å2
Baniso -1Baniso -2Baniso -3
1--9.4306 Å20 Å20 Å2
2---9.4306 Å20 Å2
3---18.8612 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: final / Resolution: 2.2→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 109 90 2294
Biso mean--81.57 77.66 -
Num. residues----267
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d817SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes352HARMONIC5
X-RAY DIFFRACTIONt_it2234HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion296SEMIHARMONIC5
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_contact2681SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2234HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2997HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion17.47
LS refinement shellResolution: 2.2→2.22 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.1904 42 6.47 %
Rwork0.2057 607 -
all0.2045 649 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 48.0863 Å / Origin y: 72.1494 Å / Origin z: 30.8704 Å
111213212223313233
T-0.0049 Å20.0909 Å20.0073 Å2--0.1495 Å2-0.097 Å2---0.1413 Å2
L1.2975 °2-0.2162 °2-0.329 °2-0.6592 °20.1546 °2--2.6299 °2
S-0.0362 Å °-0.3713 Å °0.2451 Å °0.2383 Å °0.0181 Å °0.0699 Å °-0.6925 Å °-0.2591 Å °0.0181 Å °
Refinement TLS groupSelection details: { A|* }

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