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- PDB-9gv1: NavMs F208L bound to sevoflurane -

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Basic information

Entry
Database: PDB / ID: 9gv1
TitleNavMs F208L bound to sevoflurane
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / Voltage-Gated Sodium Channel
Function / homologyVoltage-gated cation channel calcium and sodium / voltage-gated sodium channel complex / voltage-gated sodium channel activity / Voltage-dependent channel domain superfamily / Ion transport domain / Ion transport protein / : / PHOSPHATIDYLETHANOLAMINE / Ion transport protein
Function and homology information
Biological speciesMagnetococcus marinus MC-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHollingworth, D. / Wallace, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government5R01GM058055-24 United States
CitationJournal: To be published
Title: NavMs F208L bound to sevoflurane
Authors: Hollingworth, D. / Wallace, B.A.
History
DepositionSep 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7487
Polymers31,1291
Non-polymers2,6196
Water91951
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)134,99228
Polymers124,5154
Non-polymers10,47724
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
Buried area24300 Å2
ΔGint-241 kcal/mol
Surface area48480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.703, 108.703, 209.157
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ion transport protein


Mass: 31128.680 Da / Num. of mol.: 1 / Mutation: F208L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetococcus marinus MC-1 (bacteria) / Gene: Mmc1_0798 / Details (production host): pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: A0L5S6

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Non-polymers , 5 types, 57 molecules

#2: Chemical ChemComp-2CV / HEGA-10


Mass: 379.489 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C18H37NO7 / Comment: detergent*YM
#3: Chemical ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C40H80NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-A1IPI / sevoflurane / 1,1,1,3,3,3-hexakis(fluoranyl)-2-(fluoranylmethoxy)propane / sevorane


Mass: 200.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3F7O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 7.5 / Details: 30.8% PEG300 100mM HEPES 100mM NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 5, 2023 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.2→48.2 Å / Num. obs: 32204 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Net I/σ(I): 28.6
Reflection shellResolution: 2.2→9 Å / Mean I/σ(I) obs: 4.5 / Num. unique obs: 2748 / CC1/2: 0.973 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.2 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.558 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.154 / ESU R Free: 0.149 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.252 1656 5.143 %
Rwork0.2214 30546 -
all0.223 --
obs-32202 99.953 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 66.684 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å2-0 Å2
2--2.31 Å2-0 Å2
3----4.619 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1966 0 92 51 2109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122104
X-RAY DIFFRACTIONr_angle_refined_deg2.1271.7982839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8735255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.635513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43210342
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.4371076
X-RAY DIFFRACTIONr_chiral_restr0.1430.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021482
X-RAY DIFFRACTIONr_nbd_refined0.2360.2928
X-RAY DIFFRACTIONr_nbtor_refined0.320.21462
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.27
X-RAY DIFFRACTIONr_mcbond_it7.8076.4571017
X-RAY DIFFRACTIONr_mcangle_it10.29611.5281270
X-RAY DIFFRACTIONr_scbond_it9.2746.8171087
X-RAY DIFFRACTIONr_scangle_it12.66412.2921568
X-RAY DIFFRACTIONr_lrange_it13.96866.583161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.2971200.2462198X-RAY DIFFRACTION100
2.257-2.3190.2621170.2312175X-RAY DIFFRACTION100
2.319-2.3860.2591410.2162080X-RAY DIFFRACTION100
2.386-2.4590.232990.1942057X-RAY DIFFRACTION100
2.459-2.540.2181070.181976X-RAY DIFFRACTION100
2.54-2.6280.22890.2051937X-RAY DIFFRACTION100
2.628-2.7270.2111000.1981857X-RAY DIFFRACTION100
2.727-2.8380.246950.2041808X-RAY DIFFRACTION100
2.838-2.9640.251980.1951720X-RAY DIFFRACTION100
2.964-3.1080.2391050.2071631X-RAY DIFFRACTION100
3.108-3.2760.266910.2271572X-RAY DIFFRACTION100
3.276-3.4730.262860.241497X-RAY DIFFRACTION100
3.473-3.7120.268740.2191409X-RAY DIFFRACTION100
3.712-4.0070.228580.2051320X-RAY DIFFRACTION100
4.007-4.3870.23630.2141230X-RAY DIFFRACTION100
4.387-4.8990.198600.1851116X-RAY DIFFRACTION100
4.899-5.6470.237570.214995X-RAY DIFFRACTION100
5.647-6.8930.352460.265852X-RAY DIFFRACTION100
6.893-9.650.258340.245687X-RAY DIFFRACTION100
9.65-48.20.368160.324429X-RAY DIFFRACTION98.234

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