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- PDB-6mwa: NavAb Voltage-gated Sodium Channel, residues 1-239 -

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Basic information

Entry
Database: PDB / ID: 6mwa
TitleNavAb Voltage-gated Sodium Channel, residues 1-239
ComponentsIon transport proteinIon transporter
Keywordsmembrane protein / metal transport / Ion Channel Voltage-gated Sodium Channel
Function / homologyVoltage-gated cation channel calcium and sodium / Voltage-dependent channel domain superfamily / monoatomic cation channel activity / Ion transport domain / Ion transport protein / identical protein binding / plasma membrane / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Ion transport protein
Function and homology information
Biological speciesArcobacter butzleri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLenaeus, M.J. / Catterall, W.A.
CitationJournal: J. Gen. Physiol. / Year: 2019
Title: Molecular dissection of multiphase inactivation of the bacterial sodium channel NaVAb.
Authors: Gamal El-Din, T.M. / Lenaeus, M.J. / Ramanadane, K. / Zheng, N. / Catterall, W.A.
History
DepositionOct 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 11, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8318
Polymers29,7891
Non-polymers4,0427
Water63135
1
B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules

B: Ion transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,32332
Polymers119,1574
Non-polymers16,16628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-y-1,x,z1
crystal symmetry operation4_545y,-x-1,z1
Buried area34190 Å2
ΔGint-280 kcal/mol
Surface area41620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.772, 124.772, 189.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2412-

HOH

21B-2431-

HOH

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Components

#1: Protein Ion transport protein / Ion transporter


Mass: 29789.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arcobacter butzleri (strain RM4018) (bacteria)
Strain: RM4018 / Gene: Abu_1752 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A8EVM5
#2: Chemical
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 6.2 Å3/Da / Density % sol: 80.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 1.8 M Ammonium Sulfate 100mM Sodium Acetate pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 28623 / % possible obs: 97.4 % / Redundancy: 12.7 % / Net I/σ(I): 22.6
Reflection shellResolution: 2.4→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RVY

3rvy


Resolution: 2.4→29.884 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2487 1426 4.98 %
Rwork0.2132 --
obs0.2149 28620 96.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→29.884 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1862 0 206 35 2103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052125
X-RAY DIFFRACTIONf_angle_d0.6872890
X-RAY DIFFRACTIONf_dihedral_angle_d14.881208
X-RAY DIFFRACTIONf_chiral_restr0.043351
X-RAY DIFFRACTIONf_plane_restr0.004323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.4860.32041040.32962086X-RAY DIFFRACTION76
2.486-2.58550.35411290.29382564X-RAY DIFFRACTION92
2.5855-2.70310.26661540.25562748X-RAY DIFFRACTION99
2.7031-2.84550.23251400.20882759X-RAY DIFFRACTION100
2.8455-3.02360.21481430.1862771X-RAY DIFFRACTION100
3.0236-3.25680.23421490.19162799X-RAY DIFFRACTION100
3.2568-3.58410.20031530.17892799X-RAY DIFFRACTION100
3.5841-4.10160.2261460.18952823X-RAY DIFFRACTION100
4.1016-5.16320.24811520.20062860X-RAY DIFFRACTION100
5.1632-29.88650.27551560.23662985X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.55527.74845.23859.29872.79444.95130.26540.43120.57950.2251-0.98420.28390.39220.01710.57091.10840.08990.11221.1813-0.22350.8567-89.2814-22.3839-51.4243
21.90370.3514-0.16795.19844.50266.39220.234-0.01510.1918-0.3829-0.15070.1745-1.0689-0.4608-0.00630.7810.23440.19510.603-0.03990.6606-84.9695-32.224-68.6818
31.999-7.1122-5.79667.62744.60423.3482-0.07133.11880.9763-1.4409-0.56860.1898-0.5857-0.53480.73571.60060.536-0.3891.3099-0.01020.5293-77.7646-26.2985-82.5382
41.6011-1.06810.10632.46070.96442.2157-0.0368-0.1590.10290.0950.05770.0569-0.2740.0897-0.04390.4577-0.0469-0.00760.327-0.00680.3285-57.8216-48.217-75.5857
51.61270.03930.07642.368-0.78483.65280.1843-1.05060.32320.96040.16270.1635-0.54080.7432-0.21470.7017-0.0516-0.04390.7972-0.06360.4607-55.6379-56.8929-53.2393
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1999 through 2011 )
2X-RAY DIFFRACTION2chain 'B' and (resid 2012 through 2088 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2089 through 2096 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2097 through 2193 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2194 through 2239 )

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