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- PDB-9gtq: NavMs F208L Apo -

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Basic information

Entry
Database: PDB / ID: 9gtq
TitleNavMs F208L Apo
ComponentsIon transport protein
KeywordsMEMBRANE PROTEIN / Volatge-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 Apo
Authors: Hollingworth, D. / Wallace, B.A.
History
DepositionSep 18, 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)34,2827
Polymers31,1291
Non-polymers3,1536
Water93752
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)137,12728
Polymers124,5154
Non-polymers12,61324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2_645-x+1,-y-1,z1
point symmetry operation3_545-y,x-1,z1
point symmetry operation4_655y+1,-x,z1
Unit cell
Length a, b, c (Å)108.927, 108.927, 209.374
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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Components

#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
#2: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
#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.: 1 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 0.886 Å
DetectorType: DECTRIS EIGER2 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: 0.886 Å / Relative weight: 1
ReflectionResolution: 2.2→39.95 Å / Num. obs: 32379 / % possible obs: 100 % / Redundancy: 19.13 % / CC1/2: 1 / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→9.7 Å / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2774 / CC1/2: 0.954 / % 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→39.946 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.717 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.149 / ESU R Free: 0.143 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2442 1665 5.143 %
Rwork0.2169 30709 -
all0.218 --
obs-32374 99.954 %
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: 63.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 87 52 2091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122081
X-RAY DIFFRACTIONr_angle_refined_deg2.1441.7962802
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.476512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.49210336
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4341075
X-RAY DIFFRACTIONr_chiral_restr0.150.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021470
X-RAY DIFFRACTIONr_nbd_refined0.2330.2933
X-RAY DIFFRACTIONr_nbtor_refined0.320.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1750.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1130.29
X-RAY DIFFRACTIONr_mcbond_it7.7286.1321011
X-RAY DIFFRACTIONr_mcangle_it10.56210.941262
X-RAY DIFFRACTIONr_scbond_it9.0876.4331070
X-RAY DIFFRACTIONr_scangle_it12.51111.591540
X-RAY DIFFRACTIONr_lrange_it14.11663.1423142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.2-2.2570.3071180.2722170.27123350.9370.9481000.24
2.257-2.3190.2951170.24321950.24623120.9350.9591000.219
2.319-2.3860.2451450.22420520.22621980.9640.96799.95450.199
2.386-2.4590.2241010.20420970.20521980.9690.9731000.174
2.459-2.5390.2181090.19719790.19820890.9690.97599.95210.167
2.539-2.6280.228890.20619360.20720260.970.97399.95060.185
2.628-2.7270.2071010.18918780.1919790.9740.9771000.167
2.727-2.8370.25930.19418030.19718980.9670.97599.89460.176
2.837-2.9630.242980.20117380.20318360.9610.9751000.176
2.963-3.1070.2281080.19716340.19917420.9660.9761000.18
3.107-3.2740.264880.21715760.2216640.9580.971000.204
3.274-3.4710.26880.22914950.23115830.9620.9681000.216
3.471-3.7080.266730.20214200.20514930.9580.9741000.195
3.708-4.0030.169590.19413360.19313950.9820.9771000.19
4.003-4.380.229640.20712380.20813020.9720.9741000.203
4.38-4.890.196580.17811120.17911700.9760.9831000.179
4.89-5.6320.248570.22110060.22210630.9660.9711000.221
5.632-6.8640.292480.2558560.2579040.9440.9641000.252
6.864-9.5670.21340.2166950.2167290.9790.9731000.223
9.567-39.9460.386170.3244470.3274640.9470.8741000.327

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